I would say that one of the bigger differences is that killing is usually a means to an end whereas rape is usually an end in and of itself. Thus it is in a way "given the spotlight" very unlike normal violence. When a Gm lovingly describes how "a swipe cut the mook's belly open spilling intestines across the floor, feces and blood swirts through puncture wounds as he desperately tries to force his guts back into place." then I would have just as much problem with him as if he went into great detail over how a rape was carried out.
If it is just mentioned that someone is raped int eh same context as some mook or innocent was killed then fine its a relatively realistic part of the game that can be accepted and understood. If the rape is happening to a PC well they will likely want to fight back in some way. Thus it needs to be handled with great care in the same way that mind control, torture, and other things that abridge a PC's freedom need to. There are no bad story ideas, only horribly flawed executions.