I'm not a lawyer, but I don't want to live in a country run on Roy Moore's principles. His logic renders national laws null and void at a state judge's whim, in turn making the federal government irrelevant if a state chooses.
State-level nullification, in other words, is tantamount to insurrection against the federal government. So, uh, Chief Justice Moore, are you ready to spend serious time in the federal pen? That's what you seem to be inviting.
(Having said that, I have to acknowledge that states like Colorado and California are dancing on that same line with their refusal to uphold the federal prohibitions against marijuana. Is it less harmful to society to thumb your nose at federal laws you think are stupid, than to refuse to honor a federal court decision you think is tyrannical and anti-religious? I don't know, but I wouldn't boast about the former being a more "principled" or less divisive stand.)
By the way, the logical backstop to outright nullification is for Alabama's objecting judges to take refuge in their religion: to claim that issuing a marriage license to a same-sex couple would be abetting a sin. Citing religious precept is a well-worn tactic; however, it hasn't been terribly successful in the courts, at least when carried out by bakers and photographers. I wouldn't expect the argument to fare any better when made by judges. In fact, I think judges are in an even less favorable position: unlike bakers and photographers, judges take oaths to uphold the law. If a judge's religious precepts jeopardize that oath, he must ignore those precepts or resign his post.
It'll be interesting to see what Alabama's judges do.