Cross Marian of D.Gray-Man who can convert Akuma—to assist the Exorcists, or help with a mission, but programs them to self-destruct should they attempt to kill anyone, thus destroying their souls forever. Decides to sacrifice a comrade to complete a task, and raises an orphan boy with ulterior motives. However, he loves said boy and asks himself later "Do you always have to sacrifice something to protect something else?" He apparently has done that alot—enough to question it. But he doesn't enjoy it. The author says he has hardships, got saddled with alot of trouble in the war, and hides bitter things. The character seems to be a depressed fellow that deals with his sorrows by drinking, smoking, and enjoying the sex and company of women. But don't misunderstand. He actually appreciates and respects his women, thus ruling him out as The Casanova. Along with Chivalrous Pervert, he fits the Ethical Slut trope as well. One of his dislikes being "Dirty bastards."
Gekkei in The Twelve Kingdoms has this attitude toward killing the King, Queen, and Kirin of Hou to end the aforementioned monarch's execution-happy regime, the latter two of which he kills right in front of the horrified Princess Shoukei. He feels so guilty about it that despite the rest of the court begging him to take over as an interim king until a new ruler is chosen, he refuses time and again, citing the blood on his hands. He finally comes to terms with it and steps up to the plate near the end of the series, in order to have the authority to plead with the Queen of Kyou for leniency in regards to the now-reformed Shoukei.
Naruto: Itachi Uchiha. By the age of 13, the child prodigy had chosen to become a double agent for Konohagakure's leaders, spying on his own parents and his clan to prevent them from mounting a coup. Then he had to massacre his entire clan, down to the last person (although he defied the order by sparing his kid brother) and afterwards flee the village as a wanted S-rank missing nin, just to cover up the involvement of the Village Elders in this. The irony? Itachi shed so much blood and took so many burdens onto his shoulders because he wanted to spare the world from a bloody war.
It is part of being a Regular in Tower of God to betray your comrades when you notice that they re hindering your ascension of the Tower. The Regulars get sick of this very soon.
Mahou Sensei Negima! has Negi stressing out over whether helping to protect The Masquerade was the right thing to do. Everyone else tells him that what's done is done and he should stop worrying about it. Then it happens again during the magic world arc when it turns out that the Big Badactually has a pretty good reason for what he's doing. One of the main themes of Negima is that you can't always be sure if you're doing the right thing and sometimes you just have to push forward anyway.
Wei▀ Kreuz: Dirty Business is essentially the raison d'etre for Weiss, a team of assassins who kill criminals that escape the justice of the law. All of the members of Weiss consider themselves unforgivable sinners, but do what they do in order to protect innocents.
Code Geass: Lelouch makes no bones about many of the extremes he goes to in his fight against Britannia.
The Outsiders is a team that was founded by Batman specifically for the purpose of doing the dirty jobs that had to be done, bad publicity and all.
It was later refounded by Arsenal and Nightwing, and found itself fulfilling more or less the same purpose.
And then, when the bad publicity got to be too much, Batman swooped in and took control of the team again.
Watchmen: What Ozymandias does at the end. He claims that he makes himself feel the suffering of every victim, as if it lessens the evil of what he has done. His You Have Outlived Your Usefulness moment is played in much the same way. The necessity of tying up loose ends is debatable. Though it does raise a few questions when he lets the masked heroes who confronted him live instead
Squadron Supreme: Invoked by Tom Thumb in the limited series Supreme Power: Hyperion.
In Kingdom Come, it eventually turns out that Magog himself lives and breathes this trope (as is fitting as he is a deconstruction of the Nineties Anti-Hero). He eventually has a mental breakdown during his reunion with Superman, haunted by the fact that the destruction of Kansas is his fault and that his adoring public and Superman himself just stood aside and let him slide that far.
This trope is played several times with the Senate Guard Sagoro Autem. He shoots his estranged brother to prevent him from murdering a corrupt Senator, but deeply regrets the necessity of doing so. In a strange inversion, he holds his partner and friend at gunpoint to prevent him from arresting Sagoro's son, who was an unintentional part of the assassination scheme, telling his partner that he had already alienated his wife and killed his brother for his duty, and he wasn't going to let it take his son, too.
Doctor Strange had a story arc in which he had to learn dark magic in order to defeat foes which he had inadvertently loosed while saving his friends' lives. The result was a crash-course in dog marksmanship, with Strange hating himself all the while, ending in his own self-sacrifice. (He got better).
Wolverine is often the X-Man and Avenger to do this kind of thing. In fact, it was specifically the reason why he was asked to join the Avengers. But he also disapproves of the trope if it's done by others. He explains to Cyclops that, since he is doing all the dirty stuff, everybody else has to be squeaky clean.
In The Walking Dead fanfic Better Angels, Shane copes with murdering Rick by convincing himself that the group wouldn't last if he continued leading them. He feels justified when the group stumbles upon The Prison, but it gets worse from there...
Shell Shock shows that this is one of the most defining features of War Is Hell by making a massacre of unarmed prisoners and refugees a completely unremarkable affair.
Several of the tasks Navarone has to perform in Diaries of a Madman fall under this, particularly his time in Egypt.
The Battle of Algiers: This is largely how Colonel Mathieu views his job of putting down the Algerian insurgency. "Should we remain in Algeria? If you answer "yes," then you must accept all the necessary consequences." History shows that France maintaining imperial control over Algeria wasn't necessary, though, as they ultimately withdrew and could have avoided a lot of bloodshed by doing so earlier.
In Serenity, the Operative admits that what he does is evil, and that he is a monster for doing it. When he kills a man at the beginning of the movie, it's quite evident from his face that he is sorrowful and tells the man as he dies that his is a good death, and that he did fine works for the betterment of all mankind.
In Wreck-It Ralph, when Ralph wrecks Vanellope's car, he believes it necessary to save her life, but he doesn't like doing it. Especially since he knows it looks like he was just using her to get his medal, and he turned on her when King Candy gave it to him.
That said, he doesn't really have any problems using two Unforgivable Curses on Death Eaters.
In Dorothy L. Sayers' Gaudy Night, Lord Peter Wimsey has Harriet help him draw out information from the senior university members. She tells him that she feels like Judas, he tells her it's part of the job, and she soldiers on.
In The Nine Tailors, Lord Peter explicitly calls it dirty but does recommend putting two suspect in a room together with a microphone.
The Stark family from George R. R. Martin's A Song of Ice and Fire have a tradition dating back to the days in which they were the Kings in the North; the head of the family, either the King or the incumbent Lord Stark, personally carries out every execution. Lord Eddard Stark executes a deserter from the Night's Watch at the beginning of book one. He explains why to one of his young sons afterwards.
"The blood of the First Men still flows in the veins of the Starks, and we hold to the belief that the man who passes the sentence should swing the sword. If you would take a man's life, you owe it to him to look into his eyes and hear his final words. And if you cannot bear to do that, then perhaps the man does not deserve to die."
In Lois McMaster Bujold's The Vor Game, Miles Vorkosigan tells people — even his friends — so many lies and half-truths that he feels deeply relieved when he can tell Tung that he's trying to rescue Gregor, because that's a whole truth.
In Barrayar when Drou drops into a bit of a funk after she kills a man in her first real combat experience, Cordelia tells her to treasure her guilt, because society needs people who are capable of doing the necessary evil, without becoming evil themselves.
In Dan Abnett's Gaunt's Ghosts novel Traitor General, when a resistance member freaks out, Gaunt knocks him unconscious and carries him to safety. Landerson, another member, is surprised that being a commissar, he didn't kill him, and Gaunt talks of his duty to protect mankind, even the weak and frightened — and feels a distaste for it. The truth was, he could not have left the body behind, and he might as well bring him alive, but he was saying that to manipulate Landerson.
In Blood Pact, Gaunt thinks that he's done a lot of dubious things in his day, but he particularly dislikes having let the prisoner "bleed out" the Blood Magic of the pursuing witch — out of not only himself but also Wes Maggs.
In Sandy Mitchell's Ciaphas Cain novel For The Emperor, Cain and the soldiers under him must wipe out a squad of PDF because any survivor could get out the word that they were escorting the Tau ambassadors. Although the soldiers had fired on them, they were clearly not evilly motivated and they were obviously young. Cain finds himself disgusted by it, and has difficulty working out what to say to his troopers. He finally tells the sergeant to tell them that he appreciated what they did. The sergeant says he will, with obvious sympathy, and Cain realizes it was the right thing.
In the same novel, Cain shoots two of his own people dead in cold blood just as it seems the conflict is over. They had been infected by Genestealers unknowingly.
In Caves of Ice, Cain must order the destruction of a fallen guardsman's body - to carry it would slow them down too much, there's no time or tools to bury it, and leaving it where it lay would reveal their presence to the enemy. He notes no small amount of dismay on his part.
In the short story "Sector 13," he discovers a genestealer cult. At the end of the story, amid general celebration, he's trying (unsuccessfully) to avoid thinking about all the Imperial subjects and guardsmen who're being executed because, despite being loyal, they are infected and there's no way to save them.
Later, when reasoning with the Unfleshed, Uriel says he spoke with the Emperor, who sent him. A gross oversimplification, but the Unfleshed's childish minds could not grasp his story, and he needs their help.
Later still, when Leonid persuades Uriel that he must go on without them, as they are dying anyway, Uriel agrees but still feels like it is betrayal. (Uriel got stuck between a rock and a hard place several times in this novel.)
There was every chance he was consigning these men to die, and the guilt of their deaths tasted like ashes in his mouth.
In Dan Abnett's Horus Heresy novel Horus Rising, Loken feels guilty about stripping away the consolations of their religions from the conquered, who suffer from their conquest. Horus consoles him with the hope that it will lead to more happiness in the long run. Hoo boy...
In James Swallow's Blood Angels novel Deus Sanguinius, Solus confesses that firing on the Amareo and their battle brothers had bothered him. Rafen, finding himself needing to fight and kill his battle-brothers, though for different reasons from Solus, doesn't enjoy it either.
In James Swallow's novel Faith & Fire, Verity reflects that Vaun has killed and so have she and Miriya. Miriya points out how they feel it, that they have killed.
In Rynn's World The Crimson Fists Space Marine Chapter had so many of its members killed during an ork invasion that its leaders issue an order that no space marine is to risk his life to save a civilian since preserving the existence of the Chapter is now the main priority. This does not sit well with the space marines since their duty is to protect imperial citizens. In fact it is the leaders who issued the order who are first to disobey it and risk themselves to save refugees.
In the beginning of the book a scout disobeys a direct order and as a result many space marines die. The punishment for this crime is extreme and the Chapter Master hates having to order it but he has to enforce obedience and discipline. What makes it worse is that he freely admits that had the scout succeed in the forbidden action, he would have ended a war and would have been hailed as a hero of the Chapter and his offense quietly forgiven.
In Simon Spurrier's Night Lords novel Lord of the Night, Sahaal is found by religious fanatics devoted to the Emperor. He's a traitor Space Marine, but they take him for an Imperial one, and he realizes he can use them, if — he finds choking out "Ave Imperator" very difficult in indeed.
Carpe Jugulum: In Terry Pratchett's Discworld novel, it's revealed that Granny Weatherwax feels this way about nearly every decision she's made. But she has to keep making them, so no-one else has to.
Possibly with old "Stoneface" Vimes, the only one willing to execute a corrupt, depraved king; Ankh-Morpork's last. And then he got lynched for doing it.
Over the last nine years, Emiya Kiritsugu of Fate/Zero has really come to feel that his ideal is a very unpleasant want to uphold. Example: He sets fire to a building to clear some innocent people out before destroying the foundation to kill his enemy near the top. Right after doing so he realizes that he must have gotten soft because normally he would just blow up the building immediately with everyone inside. After nine years of living as a family with his wife and daughter, he's no longer nearly so nonchalant and it's weakened him considerably.
In Margaret Ball's Disappearing Act, Maris realizes that she is Becoming the Mask when she thinks that synthesizing a pleasant but addictive substance would be a bad thing to do. (And then finds herself pondering questions about whether depriving truly wretched people of their drugs will only make their lives worse.)
In Fool Moon, Harry feels bad about not telling Kim, his apprentice and friend, what the three circles of binding do. Still, he comforts himself with the idea that she shouldn't be messing with things like that, and that by not telling her about it he was keeping her out of trouble. Things only get worse when he realizes that because he withheld this information, Kim dies at the hands of a werewolf she was trying to bind with the circles. Ouch.
In Grave Peril, killing the ghost of Kravos, even though he knew it was not a real person.
In Death Masks, Harry detests having to flee Nicodemus, leaving Shiro his prisoner.
In Turn Coat, many regard Morgan as an acceptable sacrifice. After Listens-To-The-Wind insists that Harry and Molly will not be scapegoated as well, Mai says The Merlin will not be pleased; Listen-To-The-Wind says no one should be pleased with the results of this.
In Changes Harry... does things. Uses nearly all his contacts, his powers, his options waiting. He calls in his friends, he calls in his friendly enemies, and he's willing to cross the line to save his daughter. He swallows his pride, seeks help from Ivy, Marcone, Uriel even. When not enough, he takes the mantle of Winter Knight, and kills Lloyd State. By the end of it, he even kills Susan to save their daughter. Oh, and lets not forget committing genocide on an entire vampire species. Granted, they were pretty much all monsters (except all those half-bloods that were too old to survive having the other half killed) but it was still the willful murder of hundreds of thousands.
Though he doesn't actually do it, Harry admits that if Mab hadn't made him the Winter Knight, he would have either called on Nicodemus for help in summoning Lasciel's coin or used Kemmler's Darkhallow, which involves killing a lot of people.
In Wen Spencer's Endless Blue, Mikhail stops an Attempted Rape by shooting the would-be rapist. He knows the Red also killed his foster-brother Turk — but he is still horrified that he shoot a member of his crew.
In the Star Wars Expanded Universe novel Outbound Flight, this is how Commander Thrawn feels about the deaths of the fifty thousand civilian passengers of the titular ship. (Of course, in his later-set appearances, he's much more comfortable with acts of villainy; this is almost his Start of Darkness.) Kinman Doriana isn't exactly happy about it, either, though it's unclear whether he actually cares about the deaths or he simply ends up sympathizing with Thrawn. Likely the latter, since he'd been intending to have everyone on Outbound Flight killed all along, but he says, "I'm content. I wouldn't say I'm happy."
Thrawn: No warrior ever has the full depth of control that he would like. ... But I wish here that it might have been otherwise.
In the Dale Brown novel Shadow Command, American soldiers attack a Dreamland facility and express regret that the EMP device used to disable a CID unit will also fry the operator.
All of John le CarrÚ's spy novels are based on this trope. Both sides of the cold war will do equal dirt, "for England" or "for the Revolution".
In John C. Wright's The Phoenix Exultant, Phaethon thinks that turning in Ironjay to get control of his shop is petty and mean — but he can't afford to let Ironjay take advantage of his nature.
In Rick Cook's Limbo System, Toyodo is convinced that they live in a computer simulation and will just get another run if they die. The captain knows this and, feeling ashamed, still asks him to volunteer for a hazardous mission.
In the World War II novel, The Young Lions, one of the protagonists, an American soldier stationed in England listens to a sermon, where the priest says that soldiers should treat the entire war as Dirty Business; they shouldn't be proud about the Germans they killed, they should mourn them. "Kill, if you must, because in our weakness and in our error, we have found no other road to peace, but kill remorsefully, kill with a sense of sorrow, kill with economy for the immortal souls, who leave this life in battle".
In Gene Stratton Porter's Freckles, Black Jack is taken in by Angel's Obfuscating Stupidity and flirtation, and says, "When a man's got a chance of catching a fine girl like that, he ought not be mixed up in any dirty business. I wish to God I was out of this!"
In Agatha H. and the Clockwork Princess, Wooster insinutes to Agatha that Gil's found another girl. After, he reflects that anything that separates the Wulfenbachs and the Heterodyne heir is to the good of England. So why does he feel like a cad?
"The Only Game In Town": Everard realizes that the Patrol is not maintaining the time line untampered with — they are maintaining the one where the tampering happens to suit the far-fature Denellians.
"Delenda Est": Everard lies to Deirdre about his presence in her Alternate History, and then about their ability to go back — they will not return her to it, to be blotted out with the rest of it, but he feels guilty about both the lies and the way they are consigning everyone in that history to non-existence.
In Elfhome, Riki confesses that what he did was dirty business but he'd do it again anyway; this is why he's helping Oilcan, in recompense.
In Poul Anderson's "No Truce With Kings", a newly arrived alien finds the deaths resulting from their manipulations horrible; the old hand explains it's minimizing them in the long run, though nothing will wash the blood off.
In Tom Kratman's Caliphate, Hamilton despises having to take on the role of a child slave trader as part of his mission for the CIA's successor agency, but goes through with it anyway in spite of his detestation of the institution of child slavery, due to the seriousness of the situation that caused the mission in the first place.
In Andre Norton's Ordeal In Otherwhere, Charis sees Lantee taken prisoner and flees to Bring News Back. Later, when Thorvald is ennumerating the problems, he says Lantee is probably prisoner, and she thinks he may be dead, and then that he's not mindlocked, and they may have used a Mind Probe on him. She turns pale and shaking enough to make him stop, take her hands, and tell her they must face the possibility. She tells him that she had just left him, and he assures her that she did the right thing.
In Michael Flynn's Spiral Arm novel On the Razor's Edge, when Pyati talks of how much trust Padaborn had put in Eglay, Eglay is ashamed of himself and tells him that he was supposed to maim Padaborn in what should have been a fair fight.
In the fourth Protector of the Small book, Lady Knight, Kel and her comrades encounter a patrol in enemy territory. Since their mission relies on being completely undetected and they have no time to deal with the complications of prisoners, Kel orders them to kill every enemy soldier. She knows while she says it that the decision will haunt her for a very long time.
Daughter of the Lioness involves this a lot since Aly is a spy rather than someone with a sense of honor. While she has no problems with massive deception and causing the deaths of obvious enemies, she wrestles about the problem of Dunevon and Elsren, child heirs to the Rittevon throne who could be used as figureheads for a counterrevolution. When Kyprioth solves the problem with their deaths, she's both upset and stoic about the necessity.
In Triple, the hero repeatedly blackmails, bribes, and occasionally just beats people senseless to achieve his goal- obtaining the uranium Israel needs to build an atomic bomb (it's set in 1968). But he is sickened by his own behavior every time and wishes nothing more than that he could quit and give the job to someone else. The problem is, he is the best qualified and knows it, and his nation's enemies are already developing the bomb- so he has no choice but to go on.
A Song of Ice and Fire had Jorah Mormont a brave, reasonable, and good hearted knight, once sold some poachers into slavery. All so he could provide his wifes luxurious lifestyle. Again he then acts as a spy for the Baratheons to keep an eye on Daenerys Targaryen, but later switch loyalties to her.
In Rainbow Six, Clark and Ding may be hardened special forces men no stranger to the ambiguous, but they find the Curb-Stomp Battle against the ecos so one-sided it feels like murder. Even if the ecos were planning on exterminating mankind.
Live Action Television
In the series finale of Angel, when Lorne kills Lindsey. Lindsey believed that he had undergone a Heel-Face Turn (and did for that episode anyway), but he had appeared in the past to have performed such turns, only to be wooed back to the side of evil. In Angel's view, at least, he could be not be trusted not to become evil again. This underscores the differences between the views of the good guys on Angel and those on the parent series Buffy the Vampire Slayer, as on the latter the good guys (except in one case when the person responsible had done a temporary Face-Heel Turn) never killed a potentially redeemable human for any reason other than self-defense. Just before Lorne does it, a visibly remorseful Lorne says that working for Angel has become "unsavory". The victim himself was more upset that Angel didn't even kill him personally.
Buffy did have Giles... but he'd be the first to acknowledge that he's not a good guy. And his version of self-defense is a little more... pro-active than most.
Giles: She's a hero, you see. She's not like us.
Giles smothers Ben to remove the threat of Glory's return.
No shortage of this in Babylon 5, especially surrounding Cartagia's assassination. Even Vir feels that Emperor Cartagia has to die. Bonus points: while Londo is the one who is set up to do this, it's Vir of all people who actually ends up performing the act. As Vir drowns his sorrows in alcohol later, Londo can't say Vir did the right thing, only the necessary thing—and that the fact that Vir's feeling so much anguish over the act means that he still has a good heart, for which Londo envies him.
Breaking Bad has Walt killing Krazy 8, a drug dealer that otherwise would have killed him and his famliy. In the season 3 finale, Jesse kills Gale, a replacement cook that Gus had planned to use instead of Walt and Jesse.
The page quote comes from an episode of Burn Notice in which Michael helps a bad guy blow up his even-worse-guy boss in order to save a neighborhood from her gang.
There are many, many examples in Burn Notice. He forces his mother to betray a friend in order to help him, for example, and is completely unrepentant about it (though he apologizes that it became necessary). He turns bad guys on other bad guys, helps gangs so they can help him...Michael Weston has a very white morality, but very grey methods.
British spy series Callan has a protagonist who hates his job and his boss for all the filth they make him do. Why he doesn't quit is doubtful - partly blackmail, partly a belief that the Soviets are slightly worse.
In CarnivÓle, Ben killing Lodz falls into this. Samson also does a number of unethical things, but rarely expresses remorse for them.
In Firefly, Simon Tam twice does this, once when he threatens to let Kaylee bleed to death to force Malcolm to shelter them. And once when he "pays" for the Ariel job with plundered medicine. Simon is usually a fairly nice guy and seldom shows this side of him. But he can be a Well-Intentioned Extremistabout River.
The second example is actually handwaved by Zoe when they are planning the job; those meds will be replaced in a matter of hours for the rich Core World Hospital, and the people on the Rim could really use some (at a bargain price!).
Eliot Spencer of Leverage is the team's "hitter" and is the only one on the team to physically hurt people on a regular basis. Even if nearly everyone he takes down is asking for it, and he doesn't seem to have a problem with doing what has to be done, he's the only one on a team of career-criminals-turned-Robin-Hoods who describes himself as a bad guy (and not in a way that suggests he's proud of it either).
His dialogue in the Fight Ring episode to Sophie and the Gone Fishing Job to Hardison before they return to the militia camp illustrates that he has no illusions about the nature of his work, but he also knows that he is particularly suited to it and that it's sometimes entirely necessary, so he shoulders the responsibility. He takes the pain so others don't have to, because he is the one who CAN take it.
It is revealed that in the past Eliot committed acts for which there is no excuse or justification and it is the guilt over this that drives him to do what he does. Note that it's not out of a desire for redemption, because he believes with an utter certainty that he's already damned, and has made his peace with the fact.
In Merlin, the titular wizard considers his role in helping Uther seduce Igraine to be Dirty Business.
Person of Interest features copious amounts of Dirty Business, both in the past and present. Reese was a black-on-black ops specialist for the government, Finch built the closest thing to Big Brother, and Fusco was a Dirty Cop who has apparently dumped bodies in the past. A big theme has been their struggle with how this has affected them and how helping the Persons of Interest has slightly redeemed them.
Cameron of The Sarah Connor Chronicles is perfectly willing and able to do horrible and violent things to people. She isn't inherently cruel, but she uses very cold and literally mechanical logic when it comes to dealing with threats, and will often kill people who the Connors refuse to.
In the end of "In the Pale Moonlight" he sums his actions up himself:
I lied. I cheated. I bribed a man to cover the crimes of other men. I am an accessory to murder. But the most damning thing about it all: I think I can live with it. And if I had to do it all over again, I would. Garak was right about one thing: A guilty conscience is a small price to pay for the safety of us all. So I will learn to live with it. Because I can live with it. ... I can live with it.
This is also a common theme in Star Trek: Voyager, with Janeway, Tuvok and Chakotay often taking different stances as to what is acceptable.
The first season finale of Supernatural has the first instance of the Winchesters being able to kill a demon - if they're willing to ice the innocent, possessed human too.
Dean: You know that guy I shot? There was a person in there.
Sam: You didn't have a choice, Dean.
Dean: Yeah, I know, that's not what bothers me.
Sam: Then what does?
Dean: Killing that guy, killing Meg - I didn't hesitate, I didn't even flinch. For you or Dad, the things I'm willing to do or kill, it scares me sometimes.
In seasons four and five, every time Sam drinks demon blood to fuel his powers he looks at it this way.
In the 2008 series Survivors, Tom is used as the go-to man whenever the group realizes that someone needs to be killed, whether out of mercy or otherwise. Despite the fact that it takes a toll on him, and he has been trying in his own way to escape his violent past, he goes through with it anyway because it needs to be done.
Frequently on Doctor Who and more so in the modern series, the Doctor must do terrible things in order to save the universe, his genocide of the Time Lords during the Time War being the most obvious example. There's also the ending of "The Fires of Pompeii" (doom the planet or blow up the volcano?) and what his planned lobotomy of the Star Whale in "The Beast Below". Some Classic series examples include allowing a genocide of hundreds of thousands to go ahead to prevent damaging the fabric of time in "The Massacre", killing a 'beautiful' full-of-potential Woobie, Destroyer of Worlds to prevent nuclear holocaust in "Robot", and basically any time the Doctor has to intervene in a conflict involving humans and Silurians.
Mission: Impossible has this happen frequently. The team explicitly has permission to do absolutely anything in order to complete their missions, so long as they don't get caught. However, when their plan requires bad things to happen to good people, they do try to get them back out of trouble again before they leave.
Dungeons & Dragons has a supplement featuring the Grey Guard prestige class, which was a disillusioned paladin with a loosened code of conduct, allowing him/her to do some very morally questionable things out of necessity.
Several people in Exalted have had to do terrible things for greater goods (up to and including saving the whole of Creation) while still feeling incredible guilt over it. The most prominent examples are Chejop Kejak (orchestrated the Usurpation and the Wyld Hunt) and the Scarlet Empress (followed up on saving Creation from a raksha invasion by establishing herself as the supreme and unquestionable ruler of the oppressive, albeit stable and secure, Realm, and frequently cries herself to sleep at night).
This is much of Creon's rationale in Jean Anouilh's Antigone. He is challenged at the end with the question "Why? Why does dirty work need to be done?"
In Philoctetes, the generally honest Neoptolemus must trick Philoctetes on Odysseus' behalf to go with them to Troy in order that the Greeks could finally win the war. Especially given how much Philoctetes has suffered at the hands of Odysseus and some of the other Greeks, this doesn't sit very well with Neoptolemus.
Halo: Cortana, in the final Cut Scene, asserts I Did What I Had to Do, though it's clear from her tone of voice that she's trying to convince herself and the Master Chief, not stating her actual feelings.
Inverse this is O.N.I.s job, they are the one's who pick children for the Spartan II program, and they kidnapped them and place a flash clone which will die in a few days in their place.
One of their more recent operations is creating a civil war among the Elites as a means to give the UNSC an edge over their dealings with them. It back fired one them in a huge way.
The firing of the Halos by the Forerunners. The only reason the Iso-Didact went through with it was because the only other option is the extinction of all life via angry, twisted, post-god Hive Mind abominations. To say that he was not happy about carrying it out is the Understatement of the century.
Faldio from Valkyria Chronicles justifies his shooting of Alicia to activate her Valkyria powers as needed to save Gallia. He felt guilty after he had a chance to think about his actions which led to his his Heroic Sacrifice at the Marmota.
Axel, from Kingdom Hearts, eventually moves into this territory. In Chain of Memories, he's mostly a heartless killer. Most of his victims are traitors, being punished for their actions. But Vexen and Zexion were innocent, killed apparently ( but as 358/2 Days reveals there was in fact, a purpose) on a whim. But as his friendship with Roxas develops, he starts becoming a little ashamed of everything he's done. In the end, he actually laments that he "always gets the dirty work." Right before accepting another assassination job, purposefully trying to invoke I Did What I Had to Do for the sake of his own conscience.
God of War: Kratos has no choice but to push a caged soldier up an incline to burn him alive as a Human Sacrifice. As he does so, the man begs for his life. Kratos, who has slaughtered, and will slaughter, countless people, looks outright disgusted before he begins. "The Gods demand sacrifice... from all of us." Oh, and it's not a cutscene. The player has to listen to the man's screams while pulling him up the hill themselves. Unfortunately lost in non-American versions, where the cage holds a generic zombie enemy.
Grovyle in PokÚmon Mystery Dungeon: Explorers of Time/Darkness/Sky is willing to kill (and almost does at one point) to prevent the planet's paralysis, but has no malice against his targets, even once saying "Forgive me" before attacking.
Mordin Solus of Mass Effect 2 feels this way about upgrading the genophage; while he still believes it was ultimately the best option, he's also absolutely guilt-ridden by it due to his rigid personal morals.
In Mass Effect 3, provided Mordin survived the events of the second game, Mordin goes on to cure the genophage in the third game. Not only that, depending on your dialogue choices, he may angrily confess that he made a poor decision and tell Shepard that the only way to stop him from curing the genophage is to shoot him. He is not bluffing.
Mordin Solus: I made a mistake!
The right mix of Renegade actions and Paragon dialogue will make Shepard feel this way too. Especially if you chose the Ruthless background. At one point in the sequel, Shepard is asked about Virmire. Paragon Shepard's response is angry.
Shepard: I left a friend to die that day, and I didn't do it casually.
In Baldur's Gate2 you are caught up in a power struggle between the local cartel of thieves/assassins who have a freaking torture chamber in their basement and a guild of bloodthirsty vampires who follow the sister of the Big Bad who is arguably more evil than he is. Siding with either one forces you to support a gang of ruthless criminals or monsters. There's no way to avoid it; you need the help of one of these groups to pursue the Big Bad.
In Metal Gear Solid 3 Naked Snake is sent to kill his mentor and the Cobra unit. Needless to say, he is reluctant to do so. Then it turns into a massive subversion - turns out Snake had been sent to kill the Boss because it was politically convenient, which is what drives Snake to become Big Boss.
In Hakuōki, Hijikata and Kondou arrange and enact the assassination of former comrade Itou before Itou's imperialist splinter faction can cause trouble for them or for the shogunate. Their role in the assassination involves getting Itou drunk at a "friendly get-together" before sending him off into the path of his murderers, after which they quietly discuss how lousy what they're doing is.
Hijikata: This is our duty, but it doesn't mean we have to be proud of it. Sometimes the path's dirty.
Discussed in Crysis 3, where Psycho says that Claire feeling regret for skinning him in no way absolves her of guilt.
Dawn of WarDark Crusade it is implied that the Blood Ravens actions in Kronus is to cover up the Chapters dark secrets, and they are willing to kill everyone in the planet(even the loyal Imperial Guard) to keep it secret.
Sakazaki Yuuya of Hatoful Boyfriend feels like this over killing his half-brother so his full brother could live when he was a child. He had to do it but the guilt weighs on him years later, it's one of the many things he hides under a cheerful attitude, and he's completely accepted the deed and his reasons, which gives him a kind of strength as The Atoner.
Litchi Faye-Ling in BlazBlue is set to fulfill her promise to save her friend Lotte Carmine from the fate of being Arakune, while having to withstand her ailing health due to the Boundary corruption. While she still remains a kind hearted lady, she is Forced Into Evil and had to become an NOL member under both Hazama and Relius Clover to withhold her ailing status so she has more time to save Roy, but she doesn't trust both of them and her will wavers about what she is doing. This culminates in Chronophantasma where she finally was convinced to steel her will to save Roy, but the cure cannot be procured in this world and the only way to do so is to go along with Relius to recreate the world to a point where it's still possible to save Roy by preventing him to commit the research that will turn him to Arakune. Litchi accepts it reluctantly, as she was forced to fight her friend Bang Shishigami, she did it with remorse, apologizing before having to coldly beat him up. To further how this is actually a Dirty Business, when Carl Clover decided to do the same for his own plans, Litchi warned him that he shouldn't go down the villains' path, showing that she clearly dislikes this position but it's the only way available to fulfill the promise she made, and she doesn't want Carl to suffer the same thing. Though Carl decided to bear with it anyway.
The second Masyaf Key in Assassin's Creed: Revelations shows that, after killing Al Mualim at the end of the first game, Alta´r burned the body to be certain that it wasn't another illusion created by the Apple of Eden even though it went against everything that he and the other Assassins (and the culture to which they belonged) believed in. This caused a schism in the Assassins between those who believed Alta´r was justified in this precaution and those who rallied behind Abbas, who thought that Alta´r was just trying to seize power after killing Al Mualim.
In Black Flag, Bartholomew Roberts, aka Black Bart specifically tells Edward to destroy his body after he is killed so that the Templars can't take advantage of what he is to advance their own goals.
In Girl Genius, Barry was crying when he put the locket on Agatha (in a flashback). She needs it to protect her, but it will damp her down and make her unhappy.
Juathuur: Meidar is the queen of this trope. Juar has his moments too.
In El Goonish Shive, Abraham, being a Knight Templar, considered killing Ellen to be this when he first found out the nature of the "curse" the Dewitchery Diamond had separated from Elliot to create Ellen. To make matters worse, he is only going through with it, not because he honestly believes it has to be done for some greater good, but because he swore a vow to destroy the "cursed" beings created by the diamond (he never thought about whether someone would use it to remove a relatively benign/non-dangerous curse like having their gender swapped). When he's forcibly stopped from carrying out the execution, and presented with an argument that the exact words of his vow are irrelevant (he really just promised to protect innocent people from the diamond) he seems genuinely glad and swears a new vow to seek redemption for his previous carelessness.
Most Western First Responder Triage systems use a tier of wound catagories, generally increasing in severity from Green, to Yellow, and Red with Black being... well you can guess. Some places, however, use a five tier system for major catastrophes, adding the level Blue — Patient is too severely injured, don't waste resources on him/her. Jim MacDonald can tell you all about it.