I think it's really a lot simpler. Most fantasy RPGs have combat and death simply because there is a conflict where there is no mediating authority. This is kind of central to the genre. So, "murdering" NPCs is a very small diagonal step from killing them in combat. It does not stand out.

Rape, on other hand, could hardly serve any acceptable in-game purpose (or real life purpose for that matter). Its purpose is to terrorize and psychologically maim -- something you never need to do to an NPC. An ally who rapes someone in-game is not furthering the quest, and moreover is doing something that is well outside the bounds of typical PC behavior.