Interesting points for thought and discussion have been brought up here.
Let me start off by saying I'm a rape victim/survivor/whatever-you-want-to-call-it. My situation is something that a lot of people would say ISN'T rape, because I was dating the guy who did it. (Yes, I've heard that. Apparently it's better to have a traumatic occurrence become habitual rather than be a one-time-only thing. Go figure.) I have exhibited symptoms of PTSD, among other things, for a while now. I am currently seeking help for it. That's not what I'm here to talk about, however, and I'm only mentioning it to give a little context.
As much as I will never be able to forgive all the things my ex has done, I would never actively seek to harm him in any way. In no way do his actions justify my taking revenge. This is why we have a justice system that is supposed to be cold and impartial. I was too afraid to make use of that while I could have, and even IF he had gone to prison, I would NEVER have joked about him being raped there and would NEVER have wished for it to happen to him. I wouldn't want to kill him, either, or have anyone else kill him for me. In my highly subjective opinion, in real life, I can't justify revenge rape or revenge killing. He may "deserve" it, according to others, but all I hope for is that he continues to leave me alone and doesn't harm anyone else.
As far as video games go, I'm not even offended by the Tomb Raider trailer (other than the blatant "trying-to-cause-controversy-to-boost-sales" feeling I got from it). Hell, my favorite game has a bit about rape. You don't see anything, but it's heavily implied that a minor side character was raped. This character doesn't want to discuss it, so you don't. She says she doesn't want to be seen as helpless and delicate. That's it.
I think that would be the best place to start if we're trying to discuss rape in a mature way in games. Make it something that happens to anyone but the protagonist so we can gauge THEIR reactions. Then, after people are pretty sure how to handle this in a mature way, we can talk about how to make rape happen to a protagonist. I know there are games with that sort of thing in it, but I still think we're putting the cart before the horse just a bit as far as games are concerned. What's the rush? This will still be an issue for a while, I'm sure.
Sorry for the novel. I hope I made some kind of sense...