What bothers me here is less the game itself than the whole "Left Behind" movement that produced it. It would be silly to ban the game, for example, even if it were everything its most vocal detractors claim it is. a) that would just make it more popular, b) that's called treating the symptoms.
What exactly bothers you about the Left Behind movement? The fact that a product which has found commercial success, does not share your beliefs? You seem to be inordinately worried about dominionism. Have you read any of the Left Behind works? Do you know they have absolutely nothing to do with present day Christians banding together and taking over the world? This is not present day stuff, this is not marching orders for Christians to go beat people over the head and kill infidels. All the events are a fictionalized representation of a time period after the removal of all believers from the Earth. I don't think this belief qualifies as particularly extreme in the first place, it's fairly mainstream.
Even if people take all this literally to heart, you have nothing to worry about. If that many people are actually removed from earth, the behavior of post-rapture converts will probably be the least of your worries. If you never notice a sudden mass vanishing, then those looney Christians will pretty much remain in check...no taking over, no nothing.