As horrible as the act is, and no one should disput that, it is still something that did and still does happen. As such it will continue to be used in narratives when trying to get an emotional response from the audience, be it readers of a book or other gamers in an RPG.
Generally speaking if a game is for a wider audience (so not a game with just your friends that you know the boundaries of) the subject may be alluded to, but will generally not be explicit.
As for murdering everyone because that is how you want to role play your character, if the game allows it I won't stop them. As long as the game is enjoyable and balanced if I don't murder everything with a pulse (be it blood or necromagic) then I will be a happy gamer. Conversely sometimes an NPC annoys me or does something my character does not agree with, and not having arbitrary game armor helps you feel a level of freedom even if you never take the option.
Ultimately I view the benefits gained by allowing you to kill anything, outweigh the costs of some players min maxing through the game. For that reason I am in favor of adding non-combat options, but not removing combat ones.