To be honest, I think NOTHING should be censored in ANY medium. Just put a warning on and don't sell the game to kids and it should be alright. Covering your eyes won't make the problem go away. Rape can be a powerful tool from a storytelling perspective, and it's silly that you just can't depict something that happens every day, no matter how bad it is.
Furthermore, I personally disagree with the notion in the article that "you're always the hero". You're not. Plenty of games has you as an unlikable douche. I realize that you may refer to something more of a protagonist more than a hero in the literal sense, but then the entire arguments breaks down. Killing people just for the sake of it is possible, and indeed encouraged in several games. Many games has you killing innocent people too. Sure, it's USUALLY either in self-defense or in order to save the world, but not always. GTA gives you the option to run over and kill many a civilian quite frequently. You're not forced to do so, no, but you do have the option. Shall we have a game then, where you're not FORCED to rape people, but you do have the option to do so if you really want to? Following your line of logic, this would be perfectly legitimate, since it's the player's choice. There's no way to justify rape, but neither is there any way to justify murder of innocent people.
(In before "BUT THEY GOT IN THE WAY, THAT'S WHY I RAN THEM OVER", that has nothing to do with it. The fact of the matter is that I can go out of my car, walk over to a random guy and kill him without any other worries on my mind. He didn't get in the way, I just wanted to kill him and did it.)
Rape is bad, but murder is worse. (At least rape victims can recover.) I think both should be allowed in the world of video games.
EDIT:
And if you wanna go all philosophical on this, I actually agree with Darth Vader here above me. There is nothing "wrong" about... well, anything, we only THINK it's wrong. Morality is a human construct, so it really is impossible to argue that something is objectively morally right or wrong.
That being said, I think it's possible to understand what is good for our society as a whole, and to make decision based on that. For example, one could argue that rape in games promotes rape in real life, and that we should avoid rape in real life because it's traumatic for the victims, hence it's counter-productive, as society's overall goal is to bring happiness to people, hence we should disallow rape in games. Not that I support such an argument, but to me it makes a lot more sense than the simple "Rape in games is bad because I think it is." or the ever popular "Rape in games is bad because it just is.")