Not really, it would let the god(s) have more fun killing them since they don't believe in them.
That's the point of the game anyways. In the original modes.
then someone makes atheisttown and they're zipping about in flying cars and synthesizing food for their clone army to fight the dark age armies of religion with LASERS AND ORBITAL BOMBARDMENT
When this REALLY happens it will be added as an expansion. I'm an Atheist guys, I just think this is a good Idea for a game.