When Byakuya and Renji make it clear they're willing to kill Ichigo to reclaim Rukia and restore her lost powers, Rukia turns her back on Ichigo, deliberately abandoning him and ordering him to never come after her because she knows her coldness is the only way to save him.
After Aizen kidnaps Orihime, Ichigo does this to Tatsuki by saying that his spiritual activities did not concern her and telling her, Keigo and Mizuiro to no longer associate with him. Urahara later mentions it was very naÔve of Ichigo to think coldness could stop his friends from caring about him or the situation Orihime was in.
When Isshin and Ryuuken debate which of them is the worst father, there's a strong indication that they've both been forced into this trope for the sake of protecting and preparing their sons. The reasons, especially in Ryuuken's case, have only partially been explained.
Matsumoto thinks this is Gin's most endearing attribute. After the battle with Aizen, Gin left nothing behind for her to use as a keepsake. She believes he understood that a keepsake would make her linger in the past and was therefore helping her to move on by leaving nothing behind.
Koon's tactic in Tower of God of keeping the team around Baam. At a critical point, he rescinded his loyalty to Baam. The more honorable team members stuck to Baam to be the exact opposite of Koon. It worked, just as Koon wanted it to.
In Detective Conan, one of the murder victims was an Idol Singer who was rude to his manager and his band. The reason for this was that his manager had plastic surgery to make her nose smaller, not knowing that he preferred her the way she was (and murdering him as a result) and that his rudeness was a means of coping with it. Though the anime version omits the reasoning for him being rude to his band, with said reason being that he was going to leave them and didn't want them to miss him.
Lyle Delandy (the second Lockon Stratos) in Mobile Suit Gundam 00, upon finding out that Feldt was attracted to his deceased twin brother (and was therefore showing signs of being attracted to him), acts shallow and callous towards her, causing her to slap him and run off. However, he did this so that she would not misplace her feelings for his brother onto him, and because he hates being continuously compared to his brother.
In Hekikai No AION, Seine must make the parasitic Mushi's host hate her so they kill her and excite the Mushi before take it out the host. For this, she's willing to do anything in order to save them from a worse fate.
In One Piece, the people of Nami's hometown knew that Nami was working for the Arlong Pirates for their sake. They pretended to be ignorant of her motives and acted like they hated her so she wouldn't feel obligated to keep working for Arlong.
When Bartholomew Kuma separates the Straw Hats from each other and sends them flying to different islands. Superficially this seems like a very cruel thing to do, but he actually (and intentionally) saved their lives. They were in a situation they were very unlikely to escape alive, and even if they somehow did, they weren't ready for the New World yet. Kuma not only helped them escape, but by the time they reunited (two years later), they were MUCH stronger and thus more likely to be able to make it in the New World.
In Naruto, the teachers can sometimes act like this, and it's justified given the rather unpleasant nature of the profession for which the students are training. Kakashi sets up a bell test that only two people can (theoretically) graduate from, which would split up a three-person genin team for certain, and when the would-be genin fail he threatens to starve one of them. To pass the test, the remaining two are supposed to feed the starving would-be genin, and then stand up to Kakashi when he starts screaming at them in mock anger for it. This teaches the genin that there are some things in life that are more important than the rules, a lesson they would not have learned in school. Also, Ibiki's test is another example of this. He sets up a Chunin Exam in which you have to answer ten questions, but if you or even one of your teammates gets caught cheating 5 times, your entire team fails. The questions are brutally hard, as well, and when Ibiki threatens to give one last question, he gives you the option of either backing out and thus keeping a chance to retake the exam next year, or answering the question, possibly failing, and never again be able to advance in rank! Turns out there is no last question, it's just meant to test the students' resolve. Which is also cruel to be kind, because if students don't learn how to sacrifice absolutely everything for the sake of the mission, if they students put their own futures ahead of the well-being of their teams or their villages, then they are useless as the hired hands and protectors that ninjas are meant to be.
In episode 2 of Maoyuu Maou Yuusha after finding two runaway girls, the Head Maid tells the Demon King and Hero that she always reported runaway serfs in the past. The Demon King orders her to feed them and clothe them anyway. Later the Head Maid tells the girls that she despises insects. The Hero thinks she's being incredibly cruel to them, but after a few dialogue exchanges, he begins to see that the Head Maid is actually trying to help them, and hires them to be live-in maids to help around the mansion.
In Attack on Titan, during Eren's trial, Levi proceeds to brutally beat him as a demonstration that Eren could be controlled. Levi beats up Eren so badly that even those who was previously called for Eren's execution or dissection looked uncomfortable and felt Levi was going too far. It was all an act to protect Eren. Commander Erwin uses this to convince the judge to let Eren join the Survey Corps and utilize his Titan abilities to help humanity reclaim Wall Maria. Eren recognizes this and doesn't hold a grudge against Levi for doing what he did.
In Silver Spoon, Hachiken is initially disgusted at some of the things farmers do, such as separating a newborn calf from its mother the moment it's born. However, they tell him that they do that because if the animals grow a bond, separating them later on becomes even more difficult, so it's best to do it before one can be established. Tamako also headlocks a baby calf to force feed it, because it's unfamiliar with a bottle, and will starve if it's not trained to suckle one. They also warn him not to bond with animals too closely, as they are often butchered after a short while, such as the piglets.
Sleepwalker had the ability to detect demonic possession in humans, and could use his warp vision on those people to break the demons' control over them and free the humans' minds. Unfortunately, a side effect of the beams was that the humans were briefly turned into Noodle People, and so other humans who saw Sleepwalker do this typically assumed that he was attacking them. This led to more than one fight between Sleepwalker and Spectra, at least until the Noodle People effects wore off and the woman that Sleepwalker zapped explained to Spectra what really happened.
In "The Proteus Saga" from The Uncanny X-Men, Proteus' ability to shape reality puts a great deal of fear into Wolverine. So much so, that Cyclops pushes him into a killing rage to prevent him from being permanently gunshy.
Films — Animated
In Tangled, Mother Gothel continually humiliates and belittles Rapunzel, and when she doesn't claim to be teasing, she claims to be this trope.
In Wreck-It Ralph, when King Candy tells Ralph that Vanellope becoming a racer could lead to the game world being destroyed and Vanellope dying along with it, Ralph tries to convince her to drop out of competition. When she won't listen, Ralph feels forced to destroy her car and ends up devastating her. Only later, Ralph realizes that King Candy is lying through his teeth.
In Frozen (a pattern is emerging here), Elsa distances herself from her sister Anna because, when they were children, Elsa almost killed Anna with her magical powers. Elsa purposefully neglects Anna because she's scared of hurting her again. But since Anna can't remember the incident (or Elsa's powers), she's doesn't understand Elsa's actions, and concludes that Elsa must just be mean-spirited.
Films — Live-Action
Hard Boiled: After Foxy's cover is blown and he is nearly beaten to death, another undercover agent Alan seemingly does Shoot the Shaggy Dog. It's actually a trick to convince the thugs that he has been killed by first slipping a metal lighter into his chest pocket while punching him in the gut and then using Improbable Aiming Skills to shoot exactly at it (breaking a few more ribs). It's cruel, but Foxy survives ( but not for long).
The Artist: After George Valentin's film career crashes and burns with the advent of talkies, his valet Clifton remains in his service, even though Valentin hasn't been able to pay him for a year. Valentin coldly fires him and kicks him out of the house, in order for Clifton to find a better employer.
Pool Of London (1951): Near the end of the film, Dan (played by Bonar Colleano) abruptly brushes off his loyal sidekick Johnny (played by Earl Cameron). Johnny assumes it is for racial reasons but actually Dan realizes that he (Dan) is likely to be arrested and wants to distance Johnny from his problems.
Pirates of the Caribbean: In the second film, Will is ordered to be flogged for a mistake on Davy Jones's ship. When it comes out that Will is Bootstrap Bill's son, Jones orders Bootstrap to carry out the flogging himself. Initially, Bootstrap refuses, but when Jones threatens to have the boatswain do it instead, Bootstrap obliges. Later he explains to an angry Will that the boatswain is an expert flogger who "prides himself on cleaving flesh from bone with every blow". Therefore, doing it himself spared Will even greater pain.
The Dollmaker, published in 1954, has a scene where the title character slices open her child's throat with the knife she uses for whittling. She's hitched a ride with an Army general, and he's horrified, calling her a murderer — but the child is choking to death from croup, and the Dollmaker cut his (her?) throat to bypass the obstructed part of the windpipe so the kid could breathe while they head for the hospital.
Enderís Game: Ender's entire journey through battle school, where he endures pure physical, emotional, social torture ends up making him an epic commander and thus saves all of humanity. For specific examples, he is intentionally set up to be ambushed by a bully and his gang in the showers...so he'll realize that no one will help him and he needs to come up with a solution, which ends with him killing the bully. He is manipulated with coerced letters from his sister Valentine, so he won't simply write off all of humanity being as bad as his brother Peter and will therefore kill the Buggers as needed. He is placed in games that have unfair rules set up against him (such as low preparation time, more enemies on the other side, etc.) so Ender will start thinking less in terms of how to follow the rules and more in terms of how to win, which ends up helping him when he must participate in simulation not! games where the Buggers have every advantage against him. There is a virtual reality game set up for him called the Giant's Drink that is intentionally designed to be impossible to win, so Ender will start looking for third options to screw the game over, a sentiment which culminates in him bombing the Buggers out of existence and taking his own, actually real, soldiers out with them.
Harry Potter: Several things done by both Dumbledore and Snape:
Dumbledore's actions include giving Harry to the Dursleys (to be kind, since the Dursleys have magical wards around their house that protect Harry from Voldemort), not making Harry a Prefect (to be kind, since Harry gets so much positive and negative attention already that Dumbledore didn't want to add to his burden), and generally avoiding Harry during his fifth year (to be kind, since if Harry asked Dumbledore too many questions he might find out about the prophecy in the Ministry, tip Voldemort off about it through his mental connection, and give Voldemort an opportunity to lure Harry into a trap...which is exactly what happens when Harry does find out about the prophecy).
Snape's actions are more extreme, with slicing off George's ear and, of course, killing Dumbledore at the top of the list.
Granted, the flashback seems to paint George's severed ear as something of an accident and not an overenthusiastic cover act.
Also, Snape counts as a "meta-example" of this trope in which the author was cruel to be kind. At one point during an interview, J. K. Rowling was asked why Dumbledore even allows Snape to be a teacher of children if Snape isn't going to enforce the rules fairly and if Snape is going to behave like a jerk. Rowling responded that that was exactly why Dumbledore let Snape stay on: because Dumbledore wanted every child to learn at some point that not every authority figure can be trusted, and they'll have to figure out a way to deal with that eventually. All of the other teachers are relatively nice and are more than fair in their judgments; if there wasn't at least one teacher like Snape, children might grow up mindlessly trusting authority figures their whole lives because of only "good teacher" examples to draw their frame of reference from.
McGonagall has a moment of this in the very first Harry Potter book. She catches Harry, Ron, Hermione, and Draco out of bed after hours and takes away one hundred and fifty points, and from her own house at that! (She also takes fifty points from Draco, though, since he too had to be out of bed after-hours in order to even know what the other three were doing; there was no other way he could then have informed the professor about their rule-breaking.) Her reaction is justified when you consider: one, during this particular school year there was a lethal monster in the school in addition to Voldemort being after the stone, and ultimately McGonagall doesn't want the students to consider wandering around after-hours to be acceptable. Two, part of the reasons the Slytherins all come off as such jerks is because Snape plays favorites and never takes any points away from a Slytherin student, no matter how awful. McGonagall's willingness to cost her own house the House Cup, by contrast, teaches the Gryffindor students that ethical behavior is determined by the choices you make, and not the groups to which you belong. Three, the students were willing to break rules was in part because Snape only ever punished Harry for breaking rules out of a personal vendetta, so the students understandably came to the conclusion that the rules couldn't be trusted. The fact that McGonagall had a legitimate reason to punish them and the fact that she punished Draco along with them (something Snape would never have done) drove home for the students the fact that just because one teacher is a jerk, doesn't mean they all are.
"Kingsmeat": An Orson Scott Card short story featuring an alien species that conquers planets with human populations and devours all inhabitants. On one such planet one of the intended victims offers to cut off parts of selected humans and cook them for the aliens' meals, leaving him dishonored and loathed among his fellow humans. However, this offer prevents the aliens from actually killing the entire population, so, in effect, the dishonored man saved his planet.
Percy Jackson and the Olympians: Features this as a major plot thread. "Demigods", born from the union of a mortal and a god, suffer serious angst because their immortal parent rarely acknowledges them. The gods usually have very good, compelling reasons for not contacting their kids.
Twilight: Bella deliberately picks a fight with her dad, using some of the same words that her mother did when she left him, before storming out of the house, so that James won't go to her house and kill her dad.
In Jeeves and Wooster, Jeeves to Bertie. He snarks at Bertie, manipulates him, gives him the cold shoulder when he most wants sympathy, gets him into trouble, and destroys his stuff. Why? Because he cares.
The In Death series: Being a murder cop has this trope as part of Eve's job description. She has to interrogate witnesses, and pull no punches, even if said witnesses are her best friend and her aide's (later partner) brother. She has to tell families that one of their members is dead. There was one book where she had to tell this one person of interest to her face that the man she had sex with was her birth father, because she had to find out if she knew and if she murdered him. Another book had a person of interest saying about how terrible it must be for her to see only the worst in people. This is why being a cop can suck.
With all of the really scary magic out there, Harry Dresden knows which lines to toe and which to burn. Most of the lesser talents of Chicago don't, so he thinks he's being this trope when he refuses to teach one about a certain kind of Ward. He had misunderstood the Ward's purpose, so her lack of knowledge ends up getting her killed.
Most wizards, Harry's godmother Lea, and Mab, Queen of Air and Darkness argue that wizard training must be this because that's the only way to get good enough to survive. Anything else leaves them incorrectly thinking they're prepared, which is a major disservice. Harry learned to shield with baseballs? Luccio taught Morgan to shield with rocks. Lea teaches Molly after Harry's apparent deathto fight by pitting her against real enemies. Mab teaches Harry Dresden, Winter Knight with months of surprise attacks of at least that lethality, but more inventiveness.
It's a mark of how crappy the world is that they appear to be completely right.
It's another mark of how crappy the world is that the entire entry should have the Training from Hell trope attached to it.
In The Five People You Meet in Heaven, World War II veteran Eddie has suffered his entire life with his leg injury from the war. When he dies and goes to heaven, he meets five people, including his former captain in the army, called The Captain. The Captain reveals that he was the one who shot him in the leg in the Philippines so that he wouldn't get burned alive trying to save a villager from a burning house.
Live Action TV
Sliders: In one episode, our heroes pop into a new universe to find a woman trying to force her child off of a high balcony. They try to stop her, but she succeeds in pushing him off...only to have him sprout wings and fly around. The woman shrugs at the confused protagonists, saying "It's the only way they learn."
Star Trek: The Original Series: The episode "A Private Little War''. Mr. Spock is using a form of self-hypnosis to concentrate all of his metabolic activity into healing a wound. As he tries to fight his way out of it he asks Nurse Chapel to hit him, because the pain will help him back to consciousness. This leads to some confusion for Mr. Scott who doesn't understand that the slapping is actually helping Spock.
The episode "A Taste of Armageddon" has Kirk destroy the computers that are used to prevent all out nuclear war. This is a good thing because the two sides were using those computers to sanitize war by peacefully euthanize their populations (simulating various battles and strategies) in a cheaper and less destructive way. Kirk points out that war is supposed to be a miserable experience so that you do everything you can to avoid it. Make nuclear war possible, they have a reason to actually end the conflict.
True Blood: When Eric Northman imprisons a kicking and screaming Sookie and chains her up in his creepy basement, she does not know (and he does not bother to tell her) that it's all part of his plan to save her and other peoples lives by using Sookie's blood as bait. He also wants revenge for himself, so itīs not a completely altruistic act, but his cruelty still serves a higher purpose with clear benefits for Sookie in the end, i.e. her staying alive.
In Burn Notice, Michael state that you have to be cruel to be kind when in hostage negotiations, because if you show too much sympathy for the hostage, you're going to give the hostage taker leverage. If you show you're willing to let them kill the hostage if they're too badly hurt, you've gained an advantage, as hostage taking is a business, where there is only one buyer for each product.
Neal says these exact words in White Collar before intentionally turning off a woman he was flirting with to get a lead on a case. He is too much of a gentleman to pursue her interest and can't tell her what his true intentions are, so he settles with cheerfully informing her that she is the first women he's had a drink with since getting out of prison. She leaves.
On The X-Files, Scully shoots Mulder in the shoulder to prevent him from shooting Alex Krycek. Why? Because Krycek shot Mulder's father and is framing Mulder. If Mulder shoots him, there will be no way to prove that it wasn't Mulder. Though a little Not Himself because of a tainted water supply in his apartment, Mulder is eventually grateful that Scully is a good shot and apparently missed doing much permanent damage.
In the episode "Untouched", Wesley intentionally provokes Bethany by suggesting they send her home to her father. This reveals the circumstances of her powers to Angel so he can help her. In fact, Wesley can be surprisingly ruthless, willingly sacrificing his allies or sending men to their deaths as part of a grand design. In his own words:
Wesley: "You try not to get anybody killed, you wind up getting everybody killed."
In the episode "Double or Nothing", Gunn, thinking he is about to die, starts insulting Fred during a date and breaks up with her to make sure she won't mourn him as badly when he is gone.
Hawkeye did this to a patient on Mash once. A soldier was brought in who claimed to be paralyzed, but had no physical injuries. After consulting on the phone with Sidney Freeman, Hawkeye point-blank tells the soldier there's nothing wrong with him and to get up. He also refuses to issue him a bedpan or have food brought to him. Eventually, the soldier comes around and Hawkeye apologizes for the treatment he gave him.
Doctor Who: In "The Arc in Space", one of Tom Baker's first story-lines, Sarah Jane Smith had to make her way through a narrow passage to reach the Doctor. When she got stuck halfway through, the Doctor began berating Sarah Jane as "useless", which angered Sarah Jane enough for her to push her way out of the passage, just to give the Doctor a piece of her mind. Once she cleared the passage, the Doctor assured her that he only said what he did to "encourage" her, and that he was very proud of her.
In "The Curse of Fenric", the Doctor (at this time portrayed by Sylvester McCoy as something of a Manipulative Bastard) intentionally broke Ace's faith in him as part of strategy to destroy a coven of psychic vampire-like beings.
He also broke Amy's faith in him in "The God Complex" in order to save her from a monster that used faith to control its victims
BabylonFive Season 4 Episode 19 "Between the Darkness and the Light" Lyta puts Garibaldi through a deep scan breaking the blocks Bester put in his mind. This chances destroying Garibaldi's mind or killing him. The alternative is that The Mar's Resistance would execute him for betraying Sheridan.
Dr. Cox on Scrubs often found himself looked upon as a mentor figure by incoming interns, main character J.D. foremost among them. He hates that people rely on him, but also likes it because it fuels his own ego. But he is often purposefully harsh to J.D. so that he will work harder just to prove him wrong, also deflating dependence on him. J.D. realized that if Dr. Cox doesn't chew him out it's because he no longer cares.
Not surprisingly, this is the subject of Nick Lowe's 1979 hit "Cruel to Be Kind"; the narrator's girlfriend uses the title phrase to justify the way she treats him ("It means that I love you").
El Gallo, in the second act of The Fantasticks. "We all must die a bit before we grow again... I hurt them for that reason, and myself a little bit too."
In Sonic Rush Adventure, Blaze coldly tells Marine that she's an annoying nuisance (which is not entirely unjustified) and that she'd be a burden to them because it would be to dangerous for her to come with them to Whisker's hideout and because Sonic and Tails don't have the guts to do it. The cutscene is even explicitly called "Cruel to Be Kind."
In the visual novel Dangan Ronpa, Kyouko Kirigiri sometimes acts like this. She sometimes jerks Naegi around and doesn't tell him what she's up to...so that Monobear can be thrown off the scent and Kyouko and Naegi can separately discover secrets they badly need to uncover. In chapter 5's trial, Kirigiri tries to throw the blame onto Naegi for murder!!! But...it was ultimately for Naegi's own good; Kirigiri couldn't afford for herself to be executed since she still needed to discover the school's secrets, or else none of the students, including Naegi himself, would ever be able to leave the school. However, Kirigiri acknowledges that this particular cruelty didn't turn out kind, since she didn't expect Monobear to actually execute Naegi, although coincidentally Alter Ego saves Naegi from execution anyway.
In the PS2 game Final Fantasy X, Auron intentionally withholds crucial information from Tidus, telling him only what he needs to hear at each particular moment. This is because the only way to "shock" the rest of the group into considering how pointless the sacrifice is involves Tidus learning at the last minute that the Final Summoning will kill Yuna, then Tidus responding to it emotionally by screaming at the rest of group asking why they didn't do or say anything about this before now; do they care about Yuna as a person at all?! Tidus is also a person who is cruel to be kind, although unintentionally in his case, because he is the outsider who questions what the rest of the group would rather avoid facing, to give the group the kick in the pants they need to dispense with the Final Summoning and figure out how to beat Sin for good. Which was Auron's plan all along.
Also, It turns out Jecht, Tidus' father, made a failed attempt at this. He wanted to "show Tidus what it was like" at the top of the Blitzball championship. This is a laudable goal, but as Jecht himself acknowledges at the end of the game, his methods for achieving this goal were questionable at best, they involved repeatedly mocking and insulting Tidus so that Tidus' resulting anger would push him to improve his skills. This technically worked, since Tidus became the star player of the Zanarkand Abes, but since Tidus didn't realize Jecht didn't actually mean what he was saying, Tidus grew up with a hatred of his father to match his increased blitzball skills.
In the Galaxy Angel videogame trilogy, Ranpha Franboise can sometimes come off this way. There are several instances where Tact is having a problem with his chosen girlfriend, and Ranpha ends up verbally beating him over the head with an obvious solution. Tact himself can come off this way a few times, such as when in Mint's route in Moonlit Lovers, he solves his conflict with Mint by barging into her room using his commander authority to open the door and forcing Mint to have a frank discussion with him that makes her extremely uncomfortable. It works; the discussion ends with them hugging romantically, their conflict over.
Raz the psychic hero of Psychonauts is terrified of his father, Augustus. As circus performers, Augustus trains Raz so harshly that the boy is convinced his father hates him for being psychic. The truth is that all Raz's dad wanted was to instill discipline in his son so that his powers would not go to waste.
In the second .hack//G.U. game, once free of Sakaki's control, Atoli blames herself for much of what occurred. Haseo, having seen how low Atoli's self-esteem is, asks her how she intends to take responsibility rather than assure her it's not her fault. This serves to snap her out of her Heroic BSOD.
Endrance: Kind words are not always kind once spoken.
In Tears To Tiara 2, Hamil attempt to get Tart to leave town. If she doesn't, she'll either be captured and burnt at the stake for calling herself a Goddess, or get caught up in a rebellion. It kind of backfires in that his harsh words lead to her capture.
During Hatoful Boyfriend Yuuya is actually pretty gentle about trying to help Ryouta through his angst, but he does interrupt and cut through one of the younger dove's self-pity spirals.
Feel like writing me off as a heartless bastard yet? But ignoring me wonít change anything.
In Little Busters!, this turns out to underpin a great proportion of a certain main character's actions through the game. That is, Kyousuke was deliberately controlling the events of the dream world so as to push Riki and Rin into becoming stronger and realising what they were capable of, so they wouldn't give up once they're left on their own. Another character also claims this as their motivation, but that situation turns out to be a lot more complicated: Kanata did hurt Haruka because her family told her they'd hurt her even worse otherwise, but she also did it at least partially because they also told her Kanata would take Haruka's place as the outcast if she didn't. That she'd been conditioned into acting that way since birth probably also played a part.
The Roak Orcs of Goblins have a tradition where a young orc's most prized possession is taken away from them. This teaches the orc to accept loss as a part of life rather than allowing the loss to define their life. The Orc explaining this then tears off Duv's remaining wing, which has been the focus of her obsession.
In Family Guy after Peter's failed indoor water-slide ended with him injuring himself.
Brian: I'm not gonna call the hospital, because you won't learn anything if I do.
Sadly, Brian overestimated Peter's stupidity during that event.
In the King of the Hill episode "Movin' On Up", Hank's niece Luanne gets so fed up with Hank's demands that she moves out of his house, but the house she moves into is home to a trio of college-aged deadbeats that are even worse. Luanne calls Hank for help and advice on how to deal with her roommates...but Hank refuses to give either help or advice, pointing out that if Luanne can move out of the house to live on her own, she can solve problems on her own as well. It's a rather unpleasant response...but in this particular case it actually works, because Luanne does in fact figure out a way to make her roommates fall in line.
Some of the solutions to the problem-of-the-week in My Little Pony: Friendship Is Magic are this, although given the light-hearted tone of the show, it doesn't happen too often.
In episodes 1 and 2, "Friendship is Magic", Celestia apparently blows off Twilight Sparkle's concerns and makes Twilight Sparkle go get some friends instead... but if Celestia hadn't "blown her off", Twilight Sparkle wouldn't actually have been able to beat Nightmare Moon because to use the Elements necessary to do that, you need friends.
Fluttershy does this more often than you'd think. In "Dragonshy", she makes a dragon stop ruining Ponyville with smoke by yelling at him until he cries. In "Stare Master", she makes a cockatrice stop turning ponies into stone by threatening to tell its mother on it.
Twilight Sparkle gives Spike a nasty speech in "Owl's Well That Ends Well", but it's because she was disappointed in him and thought he was better than this. Spike unfortunately didn't see it that way.
In "The Cutie Pox", Apple Bloom gets a disease that causes multiple cutie marks to appear and forces her to act out all those talents. To get Apple Bloom back to normal, Zecora makes Apple Bloom tell the truth about having committed a theft in front of everyone in Ponyville...which is kind, ultimately, because in-context it's literally the only way to restore Apple Bloom back to normal.
"The Mysterious Mare Do Well" episode was this. Rainbow Dash was bragging about her heroics, and then graduated to actually putting ponies in danger just so she could save them and earn more praise. It was rather cruel of Dash's friends to dress up as another superhero and upstage Dash, but it's ultimately kinder than letting Dash potentially get somepony killed, and be in much worse trouble than simply being made to look like a fool.
"The Last Roundup" could also be this. It was rather cruel of Applejack's friends to follow her all the way to Dodge Junction and then repeatedly pester her until she breaks and tells them the truth about why she left Ponyville...and her reason for leaving turns out to not be justified, so it was ultimately kinder not to allow Apple Jack to keep thinking her friends would stop loving her.
Yes, the entire town shunned the Cutie Mark Crusaders after they found out who Gabby Gums was... but the ultimate result is that after the CMC apologize for spreading gossip, Diamond Tiara, the instigator of the mess, is punished for her part in the events of the episode. And it's kinder to let the CMC know how wrong it is now, before they screw up later in life.
Subverted during the season 2 finale, where Twilight spends several times accusing Cadence (who is to become her brother's wife) of being an imposter because her personality was uncharacteristic of the babysitter she knew as a baby foal. Not only does this cause her friends frustration at her actions, even Celestia becomes disappointed in her when her last accusation sends Cadence to tears, prompting her own brother, Shining Armor, to tell her off for hurting Cadence's feelings. Now this would have seemed like it was all in Twilight's head, that the people you know will not always remain the way you want them and that a harsh scolding from her brother was needed to bring her out of it. Except Twilight is absolutely correct! the Cadence she was suspicious off actually was a Changeling imposter who imprisoned the real Cadence under the caves and took her form so she could feed on Shining Armor's love and use the wedding to distract them from being taken over by her Changeling minions.
The Aesop of episode "It Ain't Easy Being Breezies". After an accident where a group of migrating Breezies are separated from the rest of the group, Fluttershy takes them in. When she tries to get them to leave, they show no interest in leaving. Finally, after saving one of them from a swarm of angry bees with more aggressive words, Fluttershy finally decides to kick the remaining Breezies out of her home to ensure that they get back to their own home. Fluttershy learns that being kind doesn't always mean doing whatever someone else wants; it means pushing them to be the best they can be.
In Ed Edd n' Eddy's Valentine's Day episode, Double D and May Kanker end up becoming Sickeningly Sweethearts due to a pair of cupids (played by Jimmy and Sarah) causing havoc. They spend the entire episode calling each other affectionate pet names, having Held Gaze sessions and generally seem really happy. When Ed and Eddy and Lee and Marie find out they're a couple, they decide to separate them, despite protests from the couple themselves. Even after Rolf "cures" everyone from the cupids, it's implied there are still some lingering feelings between them.
Most modern medical procedures fall under this category, including (but not limited to) amputations, invasive surgeries, and organ removal. They all would sound quite barbaric to someone unfamiliar with the procedure, but are being done to save lives.
Similarly, veterinarian procedures are very likely to be interpreted as an attack by the animal.
Unlike CPR (Clean, Pretty, Reliable), actual CPR is an emergency procedure for a reason. Part of the reason we have CPR (Clean, Pretty, Reliable) is because in live action media, demonstrating correct CPR techniques for the sake of showing what is correct and avoiding aforementioned trope could actually seriously harm the actor it was being done on. Among other things, the pressure of well-done chest compressions are enough to not only restart the heartbeat, but it can break the person's sternum, the rescue breathing can be enough to cause vomiting, and the combination usually causes a lot of pain for the resuscitated person later. The person doing CPR is most likely well aware of the potential consequences, but performs the procedure anyway because it can save that person's life, but only if it is done in combination with calling for qualified medical aid. CPR alone only guarantees a 2% chance of survival.
The whole point of the Mercy Kill trope: killing someone (quickly and with a minimum of pain) rather than letting them die painfully or suffer a Fate Worse than Death.
The idea of sailors not learning to swim sounds incredibly stupid and impractical in modern times, but in the age of sail, someone who could swim a little but couldn't be saved would drown slowly, while someone who could not swim at all would drown quickly. Since nobody was actually forbidden to learn to swim, this was more being cruel to be kind to yourself.
In terms of romantic relations, there are those who maintain that it is kinder to dump a romantic partner quickly and efficiently, rather than drag out the pain, if the breakup is a done deal. They hold that the pain is worse in the short term, but fades more quickly compared to false hope and dragged out melodrama. Not everyone agrees.
There the ancient proverbs to the effect that "The cut of a sharp knife hurts worst and heals quickest."
On the extremely mild end of the scale of cruelty, the "pull the Band-Aid off fast" school is all about being cruel to be kind.
One of the hardest things a parent, coach or teacher sometimes has to do is the opposite of helping a student/child overcome self-doubt. Sometimes, one has to puncture a dream, shatter a hope, because the circumstances are such that it's just not going to happen and pursuing it can even be harmful. It's agonizingly hard to be sure (usually) when such kind cruelty is necessary, and then very painful to inflict it. An example would be an offspring or student who is pretty good at baseball, say, and dreams of playing Major League Baseball. The trouble is that he's just not that good, he's not pro material and the parent or coach knows it, and knows his dream could keep him from pursuing a more realistic and achievable goal. How to tell him without being more cruel than need be? (And of course how to be sure you're right that he really doesn't have what it takes!) Similarly, a couple can be head-over-heels in love (or at least infatuation) and totally wrong and unsuited for each other, and all their relatives and friends know it. How to tell them or at least get them to think about it before they jump into something?
Some people, after asking and explaning and doing everything they can to tell them, just leave them to crash into the heartbreak. Sometimes, it's The Only Way They Will Learn.
Anyone who has owned a pet and they get too old, sick, or hurt to continue living a life without pain and suffering goes through this. Considering a number of pets live anywhere from 5-15 years, that is a lot of emotional investment you've put into them, and they into you in many cases. Sometimes "putting them down" is better.
The other half of the proverb at the beginning of the page: "And the truth hurts.".
This also applies to those who care for animals who will eventually be released back into the wild. The animal's caretakers will act as cold and uncaring towards it as possible so that when it is eventually released it will live off on its own rather than seeking out humans for food and comfort, possibly endangering them as well as itself.