Rape games are essentially interactive porn: that is their purpose, the intent behind their creation.
That having been said: porn is legal in the US, even the raping variety. So I fail to see us having any right to criticize the Japanese.
Also, one must wonder at the source of the uproar behind this: is it that the rapes are in the games, that they can be performed (as in, they are interactive), or that they are the goal?
In the case of the first option, I would like to remind everyone that rape has been a common factor used in both art, music, and movies for quite some time now (the latter especially so if you're a vivid watcher of Lifetime Movies like my mother is). So before you ban rape in games, you must ban it in all mediums.
With regards to the second option: I think that this isn't the real issue people draw with the game either. If rape were put into the game as a tool for pushing the storyline, or just as an extra option added to a sandbox game like GTA (as in, it would be a extra thing to do, and not the overall objective), people would get angry, but not as angry as they are now. That's just being realistic: we can't say NO USING RAPE to game developers, because that's discrimination against the medium. It's in the same school of thought as the Hide Your Children [http://tvtropes.org/pmwiki/pmwiki.php/Main/HideYourChildren] trope of game development, and I object to that. Why should we tell people that they can't use rape or child violence in games when they could be used to tell a story or make a point?
When venturing into the third option, I must say that my morals make me inclined to agree: rape as the goal of a game is disgusting. But should we generally ban rape in games just because of this? Or more importantly: why should we when rape is used in other forms of media?
I think that rape in games, for better or worse, is here to stay. All people can do is use their wallets to decide the context in which it is used.