I believe in religious liberty, but this is a civil job she has, and the law is the law,...
Obergefell is unconstitutional. It... IS NOT THE LAW.
Irrational grounds cannot provide justification for calling anything "law."
All grounds given for the justification of the majority decision in obergefell are irrational.
Anyone handing out marriage licenses in alignment with obergefell are breaking the law.
... but she isn't empowered to decide what the law is or isn't, should be or shouldn't be.
She is perfectly justified in deciding what is law and what's not. We all are, we do it every day routinely. In fact, the founders gave the power to judge what is and what is not law to NOOONE, not even the supreme court.
She and we are, however, on the hook for having to make a correct assessment of what is and what is not law.
We are under no moral or legal obligation to follow non-laws. We will also be punished by people pushing such things as laws, and must react to that tyrannical action in morally correct ways.