Just my .02 centavos-if I were the clerk, I would quit on principle, go to a lawyer and file a discrimination suit against the county/state-and get openly involved with a group working/lobbying for a halt to the employer discriminating on the basis of religious belief-hey, it seems to work for muslims with their hijabs/burkas/beards, etc-also, by leaving and dragging the employer into a lawsuit, the clerk makes herself heard, and lives to fight another day.
That sounds like a position I could respect!