To try to explain my thoughts on this argument, I have an example to offer. Bear with me.
Okay, so you have a game like BioShock, where there was some exploration of race in a dystopian society. This is a legitimate form of racism in a fictional setting because it's an EXPLORATION of the topic (in some form) while at the same time being integral to the storyline. This is generally considered acceptable and okay.
Now, imagine a game where you play your average hero, but in the South in the Jim Crow era. Your function in this game is simple, take down the foreign spies, any way you can. THAT is the storyline and THAT is what you're there for. But there are side adventures you can do that are in the theme of the time, and those side adventures are all about black people. You can beat blacks, shoot blacks, torture blacks, don white robes and burn crosses on their lawns, and every night you can choose one to lynch. You know, just for funsies.
Is this STILL an acceptable portrayal of racism in a game or storyline? Does it add anything to the storyline? Enhance your in-game experience? Would the people upset about this game just be big baby whiners with their panties in a wad?
The thing that is different between rape and murder, is murder--as portrayed in practically every video game ever--is you against someone who is equally well armed and equally able to fight back. In the rare instances this is not the case--Grand Theft Auto, for example--the people you're indiscriminately killing are little more than mannequins filled with blood sacks. There is no connection to these people, no reality. A friend of mine once described the pedestrians in GTA as "robbable parking meters that bleed."
So, for violence you have "fighting the dude trying to kill me" and "killing the slab-o-meat I have zero connection to or emotional investment in." And, oh yeah, non-human monsters.
But rape is a different story. Rape is the female equivalent (and remember, I said bear with me here) of the above example where you're lynching black men. You are taking an individual with zero power, holding them down, and proceeding to MUTILATE and TORTURE them. For funsies. (And for those who don't know how female parts work, yes, mutilation happens in rape; damage is done.) This is NOT an equal exchange of power. And, in order to make the fantasy work, you can't be fucking a faceless mannequin, she has to be real to you. Which means you have to IMMERSE yourself in the mind set of a man who would hand pick a helpless victim, overpower them, and then proceed to torture and shatter them.
When you kill a guy, he's dead. Game over. He feels no more pain.
But when you rape a woman...well, imagine breaking a leg. Imagine that the break sets badly. And sure, you're alive, but you can no longer run or jump or be active the way you used to, and in fact even walking for extended periods of time hurts. Imagine it aches when it rains and when the weather changes, so, out of nowhere and without warning, you will live the pain of that break again and again and again. Imagine your whole life changing, shifting, and once where you could do anything you wanted without a second thought, now every thing you do you have to plan it around the restrictions of your leg. And, in fact, some things you'll never do again.
And now imagine doing that to someone's psyche.
So yes, it's different.
And even IF you really do get your ya-yas off on the above, tell me how a rape is at all integral to a story. Tell me a SINGLE story where removing the rape scene would have derailed it. No, not even Game of Thrones would have been significantly changed had our thirteen year old princess been taken willingly. The only stories I can think where rape is integral are stories where the action of raping a woman sets her on a path to bloody, bloody revenge, and most of those are classified as Horror for a reason.
And the capper on all this is you are then showcasing games involving a violent and brutalizing crime TO PEOPLE WHO HAVE BEEN VIOLATED AND BRUTALIZED. This is not a minority scenario. According to statistics, half of all gamers are girls. And one in four of those girls have been sexually assaulted, molested, raped, or some combination thereof. And those are only the crimes REPORTED, the number may actually be much higher. Imagine being tortured, then being forced to sit down and watch as people play a game that features your torture, for funsies. And then laugh at you and tell you that you're "too sensitive" because you're upset at seeing your torture depicted as something to do for giggles.
Sure, a lot of PC is checked at the door in art. We depict racist dystopias, places where women are second class citizens, or even entire planets where life is cheap, short, and brutal. And we LIKE it that way. And I say more the power to it and long may it stay that way.
But...there are limits. There are places we draw lines. Like lynching black men for funsies. Or, one would hope, playing on the nightmares and horror of fellow gamers just so we can get a few cheap laughs.
Then again, maybe that's just me.