A few days ago I had that very discussion with one of the mods that shall not be named. S/he said that it's OK if the topic is "under discussion rather than harassment. If user was saying "you are Christian so you are evil" that would be harassment. Having debates about the nature of faith, religion, or belief structures is OK".
She also said "Context matters a lot when evaluating content so I typically read through related comments. If users are engaging back and forth I will often let stuff stand even if it gets a little heated because it doesn't seem like anyone is being actively harmed, but if a user directly insults another one or resorts to ad hominem attacks, I will start deleting content"
In other words, it's all subjective. I did ask him/her if the same insults hurled at Christians were used against any other groups (Jews, Muslims, Hindus, et.al) would those comments get axed or stay on the site? Guess what answer I got to that question - crickets.