We have thought the same thing, actually. Then we thought, what if there is not definite proof that gods exist, but there are people of strong faith? How would a mass disaster affect those people? What if after the disaster, people with strong faith provided comfort and aid to the sick, wounded and dying -- and hope to the living? Would that help them escape persecution? Maybe, maybe not.
We've got some cool things planned for "clerics" in Desolation. You've touched on some of their key points. They should be a lot of fun to roleplay in a post-apocalyptic world.