Can you imagine the uproar if this notary had refused - for "personal reasons" - to do business with Jews or Muslims,... or Catholics?
The fact is, it wouldn't even have occurred to her. So what if the bank's customers didn't share her religion? And if she had done that, the uproar would have been huge, and she certainly would have been fired.
So why would she even think of discriminating against atheists? Why is it that atheists aren't automatically included in our respect for diversity and the freedom of religion? Buddhists don't believe in your god either, you know.
As this article points out, the Supreme Court is currently hearing a case about this very subject:
This is really the same issue which the Supreme Court is deciding in Sebelius v. Hobby Lobby Stores, Inc. At stake is quite literally the ability of corporations or the individuals that work for them to legally discriminate for "personal" reasons. (We can call them religious reasons, but why bother? One need only cite a religion -- any old religion -- to qualify.) We are talking about 70 years of civil rights law being swept away in one fell swoop. If one bank employee can refuse to provide service for an atheist, why shouldn't a pharmacist be able to refuse to sell heart medicine to a Muslim?
Freedom of religion means that you can believe whatever you want in America. You can worship, or not, as you please. You can speak as you wish. You can gather together with like-minded people and try to convert the heathens, if you want.
But you still have to live in peace in a diverse nation, where other people might not share your beliefs. So what? That's none of your business. You can't dictate to your neighbors. You can't dictate to your employees. You can't dictate to your customers.
This is America. If you want to force other people to believe as you do - and that's exactly what this is all about - then move to Afghanistan and join the Taliban.