She asks a pretty harmless question (maybe she was hoping you could recommend a church?) and you suggest she's trampling on your shopping rights. She admits she thinks Jesus is coming (however behind schedule) and you go into a rant calling Jesus bullshit and her beliefs a cult and a lie.
I have to admit that at this point in the story I wasn't feeling too fond of you, but she tells you she loves you. (I guess the difference is I'm not a Christian.) You say her loving spirit results is the result of brainwashing, without which she could presumably have matched your level of dickishness. Also, she shouldn't use her job to express her beliefs, but it's fine for you to attack hers, I suppose because you're doing it on your own time and thus enjoy amateur status under NCAA rules.
Look, I can appreciate where you're coming from, but how in fourteen fucks does this help? When she tells her friends about this it will simply reinforce their hatred of atheists.
And while some churches would reject her as you say if she got into some sort of trouble, not all would. In fact, an atheist friend of mine who had fallen on hard times spent the last part of his life in a Salvation Army home. They never tried to convert him, and when he died there, his funeral was presided over by a Salvation Army minister who, in keeping with my friend's beliefs, conducted a completely secular memorial service without the slightest taint of theism except for a cross on his uniform. A secular humanist counselor couldn't have done better. I probably have way more in common with you than that Salvation Army guy in terms of beliefs, but I'd rather have him as a role model, and I'd pick the cashier over you to sit next to on a long flight.