I had a scary BSN flashback when I wandered in here. Someone please hold me.
I don't think modern notions of "atheism" have any place in a pre-modern setting, especially one where the gods are active, involved, meddlers who interact with the world. Hating gods, sure. Losing your faith in your god, and not identifying with any of them, also sure. But strong denial that any form of divinity exists whatsoever, when these divines are active in the world, has about as much place in such a setting as magical Facebook pages and pantomime Kardashians.
As for if they should get killed for XPs, I'd say only as the potential end boss of the game, on the scale of the final battle in BG2:ToB.
Atheism can exist in a setting like this. It just requires a shift from "divine entity does not exist" to "entity is not actually divine".