The Federal court overrode the state courts and you know that. The Supreme Court ruled gay marriage was legal and the law of the land. You can argue states rights all you want, but that's been tried before. The SCOTUS is basically an unelected Royal Court. The only way to avoid these sorts of decisions is impeaching the judges and putting ones we prefer on the bench (not possible at this time), a constitutional amendment limiting the power of the court (lengthy process that probably would fail), packing the court with more right minded justices (not possible at this time), or simply electing a President who nominates consistent, ideological conservatives to the bench.
That's been my problem with Trump from the outset, he isn't a person grounded in conservative ideology. We should be striving to elect someone who actually understand how important nominating judges with a long history of actual conservatism. As of now, many people are ignoring the importance of this and getting behind Trump - who is a populist protectionist with some conservative positions, but no history of being an ideological conservative.
Saying that, Trump is right on the law here. Davis is taking a stand, but the law isn't on her side and she will have to pay a price for standing for what is right rather than what is legal.
But is this issue the first one on which the court has presumed to produce positive law out of whole cloth? The traditional mode has been to nullify statutes. Then perhaps there could be a colorable Federal cause to hold a state legislature responsible to produce a certain kind of statute to take its place. But to hold a clerk responsible for conjuring an unwritten statute? That is to ask the clerk to engage in a meaningless farce.