[Legbreaker]

I'm 100% with SSC here. Consequences are the correct answer, not restrictions on possible actions.
On occasion I'll thrown in a morale dilemma, but only to make the point of consequences. If the players have been acting in such a way as to invite retribution or retaliation, then it WILL happen.
Rape, murder, child abuse, etc is all on the table, however the details will absolutely be glossed over where possible except where absolutely necessary to describe the "wrongness" of the situation and (hopefully) encourage the players to seek another path.
I've gained a reputation with players for "mindfucking" them, but really it's them that have caused the situation nine times out of ten. There's ALWAYS an "out", it's their choice to continue down that route...

I've played characters over the years who have committed some "questionable" deeds, but never done lightly and always with a thought towards the possible consequences. Executing prisoners is probably the most common thing, but again, only ever done when there's no other viable choice which won't result in worse problems later (such as the wounded person reporting who we are, what strength, etc to a force capable, and likely willing to wipe us out).

The youngest child soldier I've included as a Ref was a 13-14 year old girl who the PCs shot during a thunderstorm. At the time it would have been difficult to see more than a human figure approaching stealthily in the darkness, illuminated briefly by lightning flashes.
It was only later, in dawns light they found the girl was as young as she was, and also about 3-4 months pregnant. The weapon laying next to her bullet ridden body helped mitigate some of the horror. The player who's character fired the fatal shots did well roleplaying the horror of the situation and was extremely careful to check their targets from that day forward. The other Players in the game also took note and there was no more indiscriminate tossing of grenades around blind corners and so on...