Speaking as an athiest myself it always bothers me when I hear M5 saying that "murder is contrary to the laws of man and god".
It bothers you that someone thinks differently than you do? M-5 essentially had Daystrom's personality.
Does it bother you that he's bothered? That bothers me.
But seriously, as someone who doesn't even remotely believe in the divinity of Jesus, the Son worship of "Bread and Circuses" doesn't bother me at all. It's just the product of what the creators believed in/thought the audience wanted to see. If Turkish Star Trek had an episode where Uhura pontificated about there being one true God and one true messenger of said God, that wouldn't bother me either, even though it doesn't reflect my own convictions.
I don't need Trek as my personal philosophical echo chamber. I need it to entertain me.