Yeah, yeah, yeah. Same bullshit. Because Christian are easy target. Because devs know it would end pretty bad if they had included Allah in the game.
So you're saying that the 3 million would be the surviving force in America, that makes even less sense from a narrative PoV, that does sound like the devs would be making a statement about wanting to kill muslims if that was the case, because now you're saying muslims took over America after an apocalypse, for that to work story wise
As said before if this game was set in a country where the majority of people were Muslim it would make sense, but it's not, its American, where you still have psycho Christians on tv saying they can blow corona away. So yes from a narrative PoV having crazy Christian's running around murdering people or whatever under the guise of its gods will, its extremely plausible and makes perfect sense from where this game is set.
As for the politics I dont give a shit, it's in a America where the biggest religion is christianity, so its completely works from a narrative PoV, I'm sorry you dont get to kill muslims constantly, maybe try an assassin's creed mod, or hitman, that had a section with people wearing turbans