I have read biography after biography about Stalin. He was an atheist. Not sure why this is an issue, to be honest. He became such after reading Darwin.That's right: it doesn't matter.
Stalin's actions match with what we would expect from a violent man who wanted to eliminate threats to his power and wanted - like many theocrats - to re-shape religion according to his values.
Yes, things could be very nasty for someone in the Soviet Union whose religious beliefs didn't match those endorsed by the leader of the country, but the same could be said for a Protestant living in the Papal States... and you wouldn't say that the Pope was an atheist, would you?
He razed Churches to the ground and Protestants don't do really do that. They were just iconoclastic.