User A makes respectful on-topic comment that contains a minor, but passable religious reference that isn’t important to the discussion
User B ignores the whole content of User A’s respectful on-topic discussion just to attack the small, insignificant religious reference with completely irrelevant anti-religious diatribe
Religious flamewar ensues.
Diagnosis: Regular internet activity!
In seriousness, this is how internet flamewars have been starting since the beginning of the internet. Nothing particularly shocking here. Especially not for Reddit which is famous for this behavior.
Basically what you have discovered is the original definition of an internet troll: A griefing killjoy that doesn’t respect other users or the topic at hand just wants to force his own misguided opinions on other people. And/or someone who just genuinely thinks he’s right when he is not and acts like a dick about it.
But since this guy doesn’t look to be just baiting people and is in fact voicing his own ignorance, then good on you for calling him out. Eventually he will get the hint as other people shout him down also.
I’d tone yourself down a bit though. Rather than get personal against him, just stay calm and keep pointing out where he is wrong with facts, not anger. Attacking him with heated flames will welcome an internet fight and reflect badly on you.
Don’t worry about the reputation of Athiests. For years, the philosophy has endured these people making all Athiests look bad this way. But so far, Atheism hasn’t been ruined by these people and those same people learn eventually.