Being an atheist in a setting where divinely empowered clerics perform miracles that are miraculous even by the standards of 20th level wizards (like raising the dead) is too delusional to function as a PC.
It's like believing the moon landings are fake. When you're living in a moonbase and have seen the bottom half of the Apollo 11 lander with your own eyes.
Or believing the world is flat when you've personally circumnavigated it.
If your world is like Golarion or the Forgotten Realms or most other D&D settings you should not allow atheist PCs at all.
well, there is a little in game fluff for a nation of atheists (rahadoum). Not quite spell resistance, but relative...
As a person who rejects covenants with gods, your belief is strong enough to repel divine spells.
Benefit: You gain a +2 trait bonus on saving throws against divine spells, but you must make a saving throw even when that magic is beneficial to you.