One thing that isn't really addressed by these arguments is times where people kill innocent people. Take the scene in Modern Warfare 2 where you kill random people in an airport (that scene actually did make me feel sick by the way). They are helpless, they have no way to protect themselves, and none of them did anything to deserve it. I'd say that's a much worse situation than say, having the villain command the PC to rape someone, although I'm sure if that happened in the game it would get much more backlash than it did. Another example is Fable, and other similar games where you can kill anyone you want. There's plenty of unarmed bystanders who you can just take out on a whim.
Of course, rape is never good and killing can be acceptable, but I have to say that killing can be much worse. You have to live with the consequences of having been raped, but people
can move past it (I'm not saying that everyone is able to, but there are people who have)and even if they can't, they still get the enjoyment of living the rest of their life. Someone who is killed doesn't have that option.
For that matter, what about torture? Playing a game like Amnesia, or Fallout, you don't see the explicit acts, but you see the results and methods of the torture. And while rape is an awful act, and I'm not trying to devalue its impact, some of the methods that were used in both of those games are much worse, approaching the worst acts that I could possibly fathom. Yet those hardly garnered attention at all.
I will agree with the grey area point however. People have desires to have sex, and usually have it with it being acceptable, while killing is seen as almost always being wrong. I think the difference is that sex is something that is circumstantially unacceptable while killing is something that's circumstantially acceptable. I guess both that, and the fact that people have a desire to have sex makes it more difficult for people to instantly recognize it as wrong. Although I think that another large part of why it isn't addressed is how sex is a much more uncomfortable subject to people than killing. A rating for a movie will be boosted much more from sex than from killing.
EDIT:
ReiverCorrupter said:
I agree with you on this. If anything I see the jokes as a reinforcement of just how unacceptable the acts are. I mean seriously, you don't see anyone make a fuss about how people who make dead baby jokes think it's acceptable to kill babies. It's a completely unacceptable topic, and the absurd levels of cruelty in it is what makes it funny.