Lampshaded in Code Geass, Lelouch has only a mild reaction when he finds out that his plan to cause a landslide has buried not only enemy soldiers but also part of a town and possibly enemy medics, but when he finds out that Shirley's father was one of the individuals killed, he becomes very upset and is reminded by C.C. that most of the people who died because of him had families.
Then there is Rolo who just can't understand why Villeta Nu's upset (and fearful) with him for killing his own allies in the SIA. Rolo also kills many unnamed enemy soldiers with no problem but not the pursuing Black Knights after their betrayal.
Though that was most likely due to him spending all his effort escaping and keeping the shield up to have time to kill the persuers, rather than caring for their lives. Afterall, if he followed this trope, Shirley would have lived
Also, the countless security guards killed for doing their jobs and the employees in various fields that Lelouch manipulated with geass, including an order to kill themselves when he was done with them. Dead men tell no tales, I suppose. Some of these were in self-defense though, since they would have killed him indiscriminately. One of the people he spares, Villetta Nu, goes on to be a major thorn in his side.
El Cazador de la Bruja has gas-mask-wearing government soldiers attack the protagonists in a misguided attempt to contain a non-existent plague only to be killed off by various good and bad characters. The gas masks were a dead giveaway that they needed extra dehumanization for their murders to be even remotely justifiable as a good act.
Subverted in Eureka Seven when Renton loses self-control and beats an enemy KLF into a bloody pulp only to see a severed human hand with a wedding ring on it. Until then, he had remained ignorant of what exactly joining a group like Gekko State entailed. Afterwards he actively avoids outright destroying enemy KLFs whenever possible.
Averted in Fullmetal Alchemist, probably as a part of the whole idea of all sympathetic characters being very loyal to their friends, in contrast to the villains. When heroic characters start rebelling against the Army, they inflict injuries on mooks working for the State Military on several occasions, but none of them will kill (for characters who are soldiers, it is because the mooks are their former comrades-in-arms, for Ed, it's more because he's a Technical Pacifist). Also, the idea of "mooks don't have families" is averted in a later chapter, where "Greedling" tells members of the Army that if they have wives, families, etc. at home waiting for them, he's giving them a chance to run.
Averted in Grenadier with Rushuna Tendou, who is Vash's Distaff Counterpart. She offers everyone she meets a smile and a hug and if they try with all their might to kill her, no matter who, she sticks to her ultimate strategy of "taking away the enemy's will to fight", which involves not killing them. It doesn't work, it being what it is.
One could argue that Mobile Suit Gundam 0080: War in the Pocket is a deconstruction of this. The main characters, with the exception of Al, are Zeon pilots using mass-produced Mobile Suits. And each and every one of them is taken down in seconds by the Gundam of this series, with the exception of Bernie, who still dies by the Gundam's hands despite his best efforts. And to the pilot of the Gundam, they're just random enemies.
Lampshaded and subverted in Gundam SEED when Nicol is killed and the good guys are cheering over their victory. Kira then becomes angry that they are celebrating someones death only to have one of the crew point out that he has killed a lot of people up to this point and didn't care. This had never occured to Kira until now and afterwards vows to not kill a single person in battle which he takes to an insane degree considering some of the weapons on the Freedom Gundam. This is used against him to great effect by Shinn in Gundam SEED Destiny.
In Gundam 00 Setsuna spares Graham/Mr. Bushido after defeating him in combat, and then convinces him to not commit seppuku. This is someone who says, "Setsuna F. Seie. Eliminating/Exterminating target" before going into combat and then proceeds to, well, do a pretty good job at exterminating his targets. This might be because Graham's/Mr. Bushido's monologue where he calls out Celestial Being for the deaths of his brothers-in-arms sent Setsuna on a guilt trip.
There is a tragic example in Mobile Suit Gundam AGE. While Grodek and Flit hesitated on what to do with Yark Dore, the Diva's crew had no problem with their men slicing up UE mobile suits and throwing grenades at enemy foot soldiers. Such different treatment is exposed when, while trying to find Flit, Woolf runs into a dying Vagan soldier. While learning about the soldier's identity, Woolf seems to have befriended him as the soldier gives Woolf his necklace. He dies in Woolf's arms shortly after, causing Woolf to have a Heroic BSOD when he returns to the Diva.
This is largely due to the fact that the Diva's crew wasn't even aware that their enemies were human; many speculated that they were alien invaders and they were in pitched battle with humanoid spacesuits, whereas Woolf was not. Yark Dole's presence is part of The Reveal that the "Unknown Enemy" was Human All Along, which causes most of the cast to bluescreen.
Lampshaded in the Mazinger Z manga. After some Iron Cross soldiers are fatally injured breaking into Kouji's house to try and kidnap him, he states he wants to try and save them so he won't be a murderer (and he was very hesitant about killing them even if he was defending himself. And after getting forced to kill one, he was shaking, shell-shocked). A policeman who helped protect them points out that self defense isn't a crime, and that Kouji's using the "justification of a manga protagonist".
This is also justified since...well, they aren't exactly alive. They are cyborgs made from corpses, reanimated with a mechanized brain, programmed to obey faithfully Hell and his Co-Dragons.Empty Shell not even begins to describe it.
A case in and out of universe occurred in Naruto recently; Sasuke is pursuing Danzo, the most recent target of his ongoing quest for revenge, into a foreign country where the Kages are meeting. On the way, he is found by the Samurai in charge of guarding the area. Before, Sasuke proved capable of defeating hundreds of mooks non-lethally, but Sasuke elects instead to just kill everyone that gets in his way, slaughtering dozens of men just doing their jobs because it was quicker than not killing them. Ironically, this act is never remarked upon by other characters beyond Suigetsu noting that Sasuke is becoming more and more of a Hypocrite, and the fandom didn't consider Sasuke across the Moral Event Horizon until he stabbed Karin, a character with a name, several chapters later. To be fair, Karin was one of Sasuke's few allies. Trying to kill someone who would follow you into hell is a better indicator for crossing the Moral Event Horizon than killing people he never knew nor cared for.
In One Piece, the one thing Luffy can't stand in a man is someone who would hurt his/her own crew. While the Straw Hats themselves have no trouble bashing through people and leaving them in severe condition, Luffy's Berserk Button is pressed when he finds someone with so little care towards their own crew.
Captain Kuro was the first to show this attitude, when he not only threatened to kill everyone if they screwed up his three year-long plan, but unleashes the "Cat Out of the Bag Attack." Such an ability lets him move at high speeds, but at the cost of vision, leaving him swiping and cutting away at everyone in his crew, as well as Luffy.
Don Krieg is next. He shows a lot of care for his crew, desperately wanting food for them all after they've been left starving for so long, but if they don't follow orders, he doesn't give a crap. He orders his commander, Gin, to suffer through a poisonous gas bomb because he refused to kill someone.
Arlong is, actually, the first to subvert this. He addresses everyone in his crew as "brothers" and becomes severely pissed when he finds many men from his crew injured from Zoro.
Commander Sazabi's troops in SD Gundam Force may apply in a far less spoken version. The Zako Soldiers, by far considered the series most innocent mooks never die on screen, and are simply cast aside. The more malicious Dark Axis troops are not as fortunate, however, and very clearly explode. Tallgeese's Pawn Leos fall into a middle ground, in that they enjoy what they do, but are as Woobie-like as the Zakos, and aren't said to actually die when defeated.
Explored and subverted in To Aru Majutsu no Index, with Mikoto's "sister": a series of 20,000 clones of her made just to provide a challenge so that a "level 5" (absurdly powerful) ESPer can develop his powers to the theoretical godlike level 6 stage, just to see if it can be done. Touma and Mikoto are horrified at the idea of her clones being mooks made just to die, and nearly get themselves killed trying to stop the genocide, though over 10,000 have already died.
Averted in Trigun by Vash the Stampede who refuses to take a human life, sometimes using his Improbable Aiming Skills to shoot other people's bullets out of the air. When he gets caught flat-footed by a couple of mooks in one episode and accidentally shoots them seriously in self-defense, he's overcome with panic for their welfare, desperately trying to bandage them up first even though he was shot as well. On the Crapsack World he lives, even young teens consider this behavior immature.
In an early arc of Zombie Loan there was a woman turned into a zombie minion and subsequently re-killed. Cue the end of the arc where the main characters attend her funeral, and one of the characters saying something along the lines of "When someone dies, someone always cries for them."
Science Ninja Team Gatchaman and its translations. Played straight, subverted, played with... oddly enough, the mook that shows the picture of his family survives. But he's still back in prison serving a life sentence.