Given they changed the definition of marriage after she was employed, one would think she could be grandfathered in.
That was my very first thought as well. But as Conscience of a Conservative pointed out, the clerk is in a position to prevent all gay marriage licenses in the country from being issued. I checked on that; Conscience is correct (trust, but verify).
So even a new hire cannot issue those licenses, and that muddies the water quite a bit.
So, to me anyway, this is now looking less like a religious exemption case, and more like a states rights case.