I just talked today to a reporter in Houston who is doing a news story about prayer in the workplace. He wanted me to help him find a local spokesperson who could give a dissenting view, since all the religious folks he'd talked to were gung ho for the idea. I don't know how the article will turn out, but watch the Houston Chronicle this weekend because that's probably when the story will appear. Who knows, it may have something insightful to say.
This is tough, and they can fire a person for just about anything they want these days. In the short term you may consider looking for something to replace it. They say that employers are more likely to accept you if you are already in a position. Of coarse I hope this doesn't happen, but it may be that your next employer is more accepting.
While you are doing that, I would suggest being as good a person as you can be. Perhaps even kinder than you typically are. Thus if they do let you go they will forced to do it despite the kind of person you are. It might not be the most satisfying way of doing things, but if they don't let you go, they will learn that atheists aren't all the evil they believe we are. And if they do... Maybe you will be ready for it.
I'm sorry to hear your job is in danger. All I can say is take the high road, don't give them any excuses they can use to justify their bigoted behavior. If you do lose your job, then is the time to consider the low road: ask an attorney you trust whether you have a case.