Re: Atheism, and "Bread and Circuses"
Yes, the chapel was nondenominational. In Kirk's opening remarks at the wedding, he mentioned "our many beliefs." Seems to me that would imply that some of the crew had some sort of spiritual beliefs, maybe even religious beliefs.
Whatever GR personal beliefs, I think he was a smart enough writer to create characters that didn't share those beliefs. Life, both fictional and real would be pretty boring if everyone was the same.