I'm curious to the ones complaining... would you feel the same if Nintendo blocked a game for it's gay bashing? If that's somehow different, then you need to check your hypocrisy.
I'm sorry, but that's a rather miserable comparison.
Religious people are constantly trying to associate themselves with other maligned groups of people in some deranged attempt to confuse the public that religion deserves some sort of special protection and reverence. Stupid and wrong is stupid and wrong. Cloaking it in "religion" doesn't suddenly make it a protected idea that none shall critique. Especially if that belief is not only wrong, but encourages or even mandates discrimination and hate.
Religious people like to shut down criticism by asserting that their belief in insane mumbo-jumbo is above questioning and criticizing and that for you to do so is intolerant. Further, that your intolerance of their intolerance makes you just as bad (it doesn't; tolerance of intolerance makes you a coward).
So, in short, suggesting that criticizing the absurdities of religion is on par with hatred, discrimination, and violence toward people because of their sexuality (or ethnicity, skin color, or any of the other things religion tries to cling onto in its pathetic defense) is pretty intellectually offensive.
Now, if this was a game about strapping on a flamethrower and heading out to the crowded NYC streets to start melting the faces off of Christians and Muslims and other assorted lunatics, then it would be a different issue.