Clyntahn cannot be an atheist - no one outside the inner circle can be an atheist on safehold.
There was even an text sequence explaining to the one person of the inner circle considering himself to have become an atheist that he had to look up the explanation in a federation book to even understand what atheism is.
"Atheism" means that the person believes that no gods exist - but on safehold the entire population knows for a fact that god exists, proven by the existance of the main temple, dozens of artefacts that cannot have been made by mortal means and thousands of experience reports and books of mortals who have met and talked to the archangels.
Therefore all safeholdians might disagree with some ideas that were supposed to be given by god, and they can agree or disagree with the church, but they cannot deny the existance of god - it's simply not possible in their frame of reference.
Clyntahn knows that god exists and will judge everyones soul after their death - he is just delusional in believing that his version of everything is what god wants.
