I looked at many comments in that thread when the conversation was linked in a different post. Never noticed a rule violation.
Do you really think it's against the rules to imply someone's religion isn't real? I would be much more concerned if comments like that were censored.
We're all here to talk about stuff. That's what's happening here.
Guess I'm just shocked that such a comment would be removed. Seems harmless. It changes how I think about that community.