IMO, part of the problem we have now is the use of the word "marriage" in government and civil affairs.
IMO, the word "marriage" should be left up to churches to define and decide who they will bless or "marry" in their membership populations.
If we inserted the word "civil" before the word marriage in State, federal, and local rules, regulations, and laws, or substituted some other phrase that omits the word marriage, a lot of these religious issues would be moved back into religious institutions where they belong, IMO. Government agencies should not be in the business of licensing "marriage". They should be in the business of determining if the civil domestic union is a lawful contract, and issuing a permit.
All citizens would then be free to "marry", or not marry in the church/ faith/ philosophy of their choice, or not. Free to have a civil domestic union contract, or not. Free to have both. The only one that would "count" legally would be the civil union. It would be the ultimate way to "level the playing field" for everyone.
And it would more clearly define for everyone that this kind of workplace disobedience is grounds for termination for not doing your job under the law, and not some kind of religious civil rights stand.
I personally think we need to pass many more laws strengthening the separation between church and state-- our growing religious and cultural diversity as a nation will demand it, IMO.
I also think there should be many more clearly defined limits as to what kind of accommodations a civil workplace should have to make for an employee's personal religious beliefs or expressions of those beliefs. JMO.