Although I agree that rape is a touchy subject, it is appropriate for the game. If you order a band of men to kill civilians and perform wanton destruction where they can, it implies that they will commit all kinds of modern-day war crimes. We as players should abstain from being graphic, our characters as nobles shouldn't personally engage in such behavior (and we can enforce this IC with the vulgarity report option), but it is a viable option for the game setting.
The "Kill, Rape, Burn" should be a hot button topic between realms, though. Your men may kill a few guards who wouldn't stand down while pilfering tax gold (how I always saw a few villager deaths with less aggressive options), but to order your men (or for a general/marshal to order the armies) to slaughter the innocent should spark outrage and hatred. CHARACTER hatred, not player.
We play a game where we create villains and heroes. Sometimes villains do dark things.