Warhammer 40,000: after Angron was beaten back from Armageddon, the Inquisition rounded the surviving local population to be sterilised and placed in forced labour camps to prevent them from spreading first-hand knowledge of Chaos. Logan Grimnar of the Space Wolves... didn't like that very much, and has even vowed not to let this kind of thing happen again. Since it's someone in 40K making a principled and compassionate decision, doubles as a Crowning Moment of Heartwarming.
The thing is, the Inquisition haven't called him that. They're too scared of him to do it.
Under Logan Grimnar, the Space Wolves have started doing this a lot, actually. But his subordinates tend to voice their displeasure with their Boltguns instead. On of the more notable examples, an event called Honor's End, saw hundreds of Marines dead when the Space Wolves were enraged by the Flesh Tearers' butchery of civilians long after the enemy had been routed.
During the Third War for Armageddon, a group of Orks infiltrated a refugee camp. When the captain in charge of the Marines Malevolent advocated wiping out the camp with artillery to eradicate the Orks, the Chapter Master of the Salamanders very nearly came to blows with him. In fluff, the Salamanders are much more conscious of civillians, and resultingly much more careful to avoid civillian casualties, than most other chapters who often see them as "unfortunate, but they got in our way."
Exalted: In the beginning of their guidebook to Hell, a comic shows a tour guide showing the decadent First Age Solar Exalted about the Demon City, only to realize that they don't care at all:
Oh, what's the use? Nobody cares anymore. Nobody comes here for the right reasons. You're all either hiding from your responsibilities, or lost in your own little worlds. Why do we bother?
During the Time of Troubles, Helm was tasked with ensuring that the other gods did not enter a certain portal. When Mystra tried to force her way into the portal, Helm struck her down without even bothering to figure out an alternative. The resulting outrage and backlash from the other gods (not to mention his own followers) was so severe that to this day there's lingering resentment over what he did.
Helm's followers weren't too long in getting their own incident of this when an expedition of one group's led to them discovering Maztica... and promptly re-enacting "Conquistadors vs Aztecs". How bad was it? They founded an entire new order of paladins to try and make up for the damage those Helmites did.