[quote=UnseenShade]
What about atheists? I have toyed with an idea of an atheist that works to the detriment of the Imperium, but they want to get the truth of the Emperor out. (i.e. he isn't happy with religion and never wanted to be a god. He wanted humans to move from superstition and religion altogether)
[/quote]

You would be running around with guys gaining power from dark gods. You can be an atheist all you want in this universe but the gods know you exist and you are hanging out with guys who they are directing. Things are unlikely to go well for you.