"And an angel of the Lord came up from Gilgal to Bochim, and said, 'I made you to go up out of Egypt, and have brought you unto the land which I sware unto your fathers; and I said, I will never break my covenant with you. And ye shall make no league with the inhabitants of this land; ye shall throw down their altars: but ye have not obeyed my voice: why have ye done this? Wherefore I also said, I will not drive them out from before you; but they shall be as thorns in your sides, and their gods shall be a snare unto you.' And it came to pass, when the angel of the Lord spake these words unto all the children of Israel, that the people lifted up their voice, and wept."
Only barely subverted in Fullmetal Alchemist. During the Ishvalan War, Alex Louis Armstrong becomes so horrified about the genocide brought down on the Ishvalan people, that he ends up letting a couple of them escape the extermination. SolfJ.Kimblee notices this and quickly kills the two Ishvalans. As Kimblee states himself, he could easily get Armstrong in trouble by reporting him to the court-martial. However, he doesn't do this, which makes his character all the more disturbing.
In Black Lagoon, Balalaika (a Russian veteran from the Afghanistan war and current crime lord) reveals that although her discharge was medical, and on-request, she was unofficially dishonored because she saved a child from a refugee camp, mirroring Caxton stopping his superior officer in 'Nam from leading the unit to rape a young village girl.
In quite possibly one of the most horrifying uses of this trope ever, issue 11 of Transformers: More than Meets the Eye reveals that Shockwave's Start of Darkness was caused by a horrific procedure performed on him by the corrupt Senate that destroyed his personality and left him an emotionless monster with a cycloptic head and claws for hands. The reason? He objected to a plan of theirs that would've killed thousands of innocent people and allowed the heroes to prevent said plan.
Occurs to Hiccup in Dreamworks' How to Train Your Dragon, when his father discovers that Hiccup's success against dragons comes from understanding them rather than ruthlessly destroying them. Once Hiccup's compassion for the Night Fury Toothless comes to light, Stoick drops the hammer: "You're not my son."
In The Hunchback of Notre Dame, Frollo orders Phoebus to burn down a mill with the miller and his family still inside. Not only does Phoebus refuse, but when Frollo sets the fire himself, he goes in to rescue the family. Frollo would have had him executed for treason right then and there, had Esmeralda not come to the rescue.
The Yeerks are a Puppeteer Parasite race that considers sympathizing with or befriending the host the worst possible crime, and their laws punish it with a painful death sentence.
The Animorphs are pretty hostile towards Cassie on the occasions when she shows sympathy towards Yeerks.
In Harry Potter and the Deathly Hallows, we learn that Peter's silver hand was enchanted by Voldemort to strangle him if he so much as seriously thought about helping Harry, which it does in the end.
In The Dresden Files, the only way for a criminal who violated the Laws of Magic to escape immediate execution is for a member of the White Council to vouch for them. This places both of them under the Doom of Damocles; if the criminal violates a Law again, both the criminal and their sponsor are executed.
Note that this specifically applies to one category of crime, which is to indulge in The Dark Arts. This is because said Dark Arts are literallyaddictive; those who so much as begin to delve into them, even for a good cause, inevitably wind up Slowly Slipping Into Evil. Thus, the requirement for a White Council member to vouch for the accused; his role is not only to demonstrate that the offender isn't evil, but to prevent them from becoming evil due to the influence and temptation of The Dark Arts.
The M*A*S*H episode "The Trial of Henry Blake" puts this into perspective: in an attempt to have Henry relieved of duty as commanding officer of the 4077th, Margaret and Frank have him charged with a number of crimes, including giving aid and comfort to North Koreans. In actuality, Henry had been contributing penicillin, among other drugs, to an elderly American nurse who runs a clinic in enemy territory dedicated to aiding poverty-stricken civilians, and was doing so long before the war even began.
The Star Trek: The Next Generation episode "I Borg" has Picard refuse to use Hugh, a Borg drone they rescued, as a carrier for a cyberweapon that would theoretically destroy the Borg Collective. He had come to see Hugh as a person instead of a mindless enemy. In the episode's sequel, "Descent", Admiral Nechayev is unpleasantly astonished at this, dresses down Picard for placing his conscience at a higher value than the lives of Federation citizens, and gives him a direct order that, if a similar opportunity presents itself, he is to take advantage of it.
Downplayed in the Star Trek: Deep Space Nine episode "Captive Pursuit". Sisko chews out Chief O'Brien for helping Tosk escape the Hunters (technically it was a minor Prime Directive violation in addition to resulting in the death of one of the Hunters). However, the Hunters had attacked Deep Space 9 to get to Tosk and the subtext of the scene makes it pretty clear that Sisko's only doing it because he's required to and that O'Brien knows it.
The Bible has a lot of examples involving God punishing His people for showing pity to those He commanded to hate and sparing those whom He commanded to destroy. To be clear, this was because he wanted the people around the Israelites gone, because otherwise they always ended up leading the Israelites into sin.
Leviticus 10:1-6: Aaron's two sons, Nadab and Abihu, were burned to death by God for offering strange fire which they were commanded not to bring. He then invokes this trope by warning Aaron that he'll kill him and the rest of the Israelites should he mourn for their losses.
Numbers 16:41-50: The Israelites complained to Moses about God burning 250 of the other Israelites to death for burning incense. God's response? He gets angry and starts killing 14,700 more of the Israelites.
Judges 2:1-4: Quoted from above, an angel of the LORD scolds the Israelites for incomplete genocide of the inhabitants of Canaan as well as being friendly with them. To punish them, God allows the Canaanites to be Israelites' oppressors.
I Samuel 15:18-23: King Saul is chastised by Samuel because he had spared only one Amalekite, King Agag, as well as the sheep and cattle which were valuable. This is where God officially rejected Saul as king of Israel, to be replaced with David.
Champions supplement Red Doom. Yuri Kamonov (AKA Sputnik) is a superpowered member of the Supreme Soviets. He won't use lethal force against opponents unless it's absolutely necessary and there's no other alternative. He also tries to avoid conflict and resolve confrontations by negotiation or non-lethal force. This has caused him to get in trouble with Colonel Vasalov, the leader of the Supreme Soviets, on multiple occasions, and Vasalov has punished him by denying him any promotion.
In Sophocles' Antigone, the title character's brother Polynices dies an enemy of the state, and Creon commands that Polynices' body shall not be buried. Antigone gives him a proper burial anyway, so she is sentenced to be locked in a tomb.
The entire plot of Disgaea 4: A Promise Unforgotten is more or less driven by the fact that the Big Bad Nemo was once a human who was injured in a war and helped by an enemy nurse called Artina, who was executed as a traitor for it (and ended up convincing Valvatorez to give up blood, allowing Nemo to take over his position). Thus leading to his Start of Darkness (and her becoming the angel Vulcanus).
In Final Fantasy IV, it's ambiguous whether Cecil is punished for expressing sympathy for the Mysidians, even though he carried out the order to take their crystal, or for questioning the King. However, Kain is also punished, just for trying to defend Cecil.
Part of the backstory of World of Warcraft's paladin Highlord Tirion Fordring. Not long after the second war against the orcs, Tirion has his life saved by one, Eitrigg. When Eitrigg is captured, Tirion tries to save his life and return the favor, only to be ostracized, declared a traitor, and exiled.
A flashback in Terra has Talos Antares try to fake having killed a human civilian to protect her from his immediate superior, Solus Kalar. Solus isn't fooled, hunts down and kills the civilian in cold blood, then starts beating the crap out of Talos (as pictured above). Agrippa Varus, Solus' equal in rank at the time, rescues Talos.
The pilot episode of TRON: Uprising has Beck hijack a train full of Programs about to be arrested by General Tessler and either killed or made to fight for the Big Bad. During the hijacking, he spares the life of a Mook, who is shocked at being spared and does a Mook-Face Turn over it. He helps Beck find and free the Programs, and seems about to switch sides when he gets a fist through his torso, courtesy of General Tessler.
In the SpongeBob SquarePants episode "The Clash of Triton", King Neptune reveals that the reason he is sad during his 5,000th birthday is because he misses his son Triton, whom he locks in a cage in the Island in the Sky for 10,000 years (although specifically, Triton has only been in the cage for 1,000 years) because he made a cure for all mortal diseases, hoping that would teach him how to be a god.
In Exosquad, the Neosapien ace Thrax is demoted for repeatedly showing mercy to Terrans, such as refusing to finish off Kaz Takagi after winning a space duel against him on Mercury and disobeying direct orders to detonate thermonuclear charges under Venus City, killing all Terran soldiers and captured civilians inside.
In The Legend of Tarzan, Hugo and Hooft are on the run from the Foreign Legion because they disobeyed orders to kill civilians.
In The Simpsons episode "The Parent Rap", Bart would've gotten this for standing up for his parents had Judge Roy Snyder not arrived just in time. He even agrees with Lisa considering that Bart, Homer, and Marge had been through enough.
Russian dissident author Aleksandr Solzhenitsyn first expressed his independence of mind as a Red Army officer during the battle of Berlin in 1945. He openly complained against the barbaric treatment of captured German civilians, especially mass rape of German women, and sought to prevent men under his command from ill-treating Germans. He also sent reports higher up the command ladder expressing his moral objections and pointing out this was not only corroding the men, it was breaking down normal discipline in the Red Army. Alas for Solzhenitsyn, this went well against official policy that had whipped the Russian soldiers up into a frenzy of hate and vengeance against all Germans. He was relieved of command, arrested, and ultimately sent to the Gulag for refusing to obey orders. Other Russians who objected to the terror inflicted on conquered Germany included war correspondents who were in a position to freely move around and witness what was being done in the name of Stalin and the Soviet Union. One in particular was given twenty-five years for "spying for the West" — all he had done was to trade stories with British and American war reporters in tripartite Berlin, telling them the horrors he had witnessed Red Army soldiers committing (Solzhenitsyn included a few characters in his books based on this story, including one fellow who ended up in the Gulag basically for talking to a British officer).
The common punishment for anyone who aided and abetted someone declared outlaw back in the day was to suffer the same punishment that the outlaw faced. Even now, harboring or otherwise knowingly assisting criminals is a crime itself.
Erin Cox, an North Andover teenager, got in trouble for attending a party despite a school policy because a classmate asked her for a ride. The police didn't take action because Cox, while committing a technical violation by being going to the party site while underage, didn't drink any alcohol herself and was preventing a case of drunk driving which could've been fatal — in fact, the police came to Cox's defense, just like many in the public who heard about the situation.
A student was suspended from her charter school for coming to class with a shaved head — as a show of solidarity for a classmate who was fighting cancer. The school quickly reversed their decision following a blazing shitstorm of justifiably angry protests, and allowed the girl to return to school.
During the Reign of Terror in the French Revolution, some of the victims got executed because they sympathized with earlier victims, called for moderation or argued for clemency. Camille Desmoullins who had initially supported the Terror as an emergency wartime measure later called for a Committee of Clemency for lighter crimes and political criminals still imprisoned. He got executed, alongside Danton (who was also becoming moderate and sympathetic but was also guilty of political corruption, for which he was charged).