I'm here to tell both parties you know SQUAT. A grain of sand in all the beaches of the earth. Let's start by conceding to our lack of knowledge and understanding, rather than being armchair experts on subjects humanity itself has no clue about.
Speaking of red herrings... What does knowledge and understanding of the universe have to do with the subject at hand? If you want to talk about being able to prove or disprove the existence of a "God", yes, it's impossible to disprove anything that isn't logically impossible. But it's impossible to disprove any idea that someone may think up. The whole existence of the "Flying Spaghetti Monster" meme was to illustrate that point. You cannot definitively prove that there isn't an invisible pink unicorn standing behind you, but if I said that there was one, I'd seriously hope you'd consider me mad.
In the same vein, if someone wants to imagine an invisible super-being, who somehow takes a personal interest in their lives and will alter the state of the universe based on their "prayers", well, yes, I can't disprove the existence of said being, but unless they have some evidence to back that belief up, then I'm going to consider them somewhat mentally unbalanced.
With that being said, I personally have no issues with this game whatsoever, if people who believe in the Christian (well, Jewish if you're talking Genesis ;)) God want to have a game set in their mythology, whyever not? No one is being forced to play it, so I can't see any problem.