Wow, that piece certainly was a breath of fresh air in a rather noxious and bad debate (from both sides). It is easy to just revel in the digust at this women's horrific views and actions, but our liberties and protections most need to be defended in these periphery cases where we are indeed disgusted because that is where they can be eroded first. Liberals seem to get that point when defending KSM, but seemingly not here.
Anyways, she has now been released due to the fact that it is clear the county is now back to continuing to issue licences via the deputies, and she has been strictly informed not to interfere. Exactly how this plays out in the higher courts is unclear, but it seems that the big harm - people unable to get married, and the added indignity to LGBT people - is removed without violating her religious principles.
I agree with the OP that according to RFRA - and will go further to say that it should be the case - that she should get a religious accommodation here, and it seems that perhaps not exactly the OPs hypothetical but somewhere in that area is indeed going to occur. I do think there is a harm still placed on the LGBT community that they have to suffer such an indignity of having procedure on a key symbol of their acceptance amended for the purposes of accomodating homophobes, but this isn't the kinds of harm typically considered in RFRA cases (compared to, say, the very obvious harm of not getting a licence). Regardless of this sentence, there is unquestionably a harm to Kim Davis by not preventing such an exemption and so it is at least debatable, and I suspect fairly clearly in her favour here, although I'm not familiar with precedent.
That said, there seems to be a range of procedural questions, whatever one suspects ought to be the end goal:
http://balkin.blogspot.ca/2015/09/fu...avis-case.html For instance, on point 5, perhaps it isn't the case that a rule even exists that needs exempting.