I hope your question about the muslim cook and pork chops is a rhetorical question. I think we all know the answer.
It is. And I'd hope that the clerk gets a good lawyer to represent her. That lawyer should document the many instances where non-Christians do get those exemptions, then demand that the clerk gets equal treatment under the law.
The trick, I think, is to find government employees who get the exemptions, as the clerk is a government official.