This is the U.S. though, so you might be surprised. There are all kinds of things that religious people can get away with that others would go to jail for. Deny a blood transfusion to your child, and that's child endangerment, at least... unless you're a Jehovah's Witness, then you're okay, even if the kid dies. Get busted with peyote, and face drug possession charges... unless you're a member of certain native religions, then everything's peachy keen (though personally, I think the drug laws are also stupid, but my only point is to show that there's a double standard).
Granted, this isn't a criminal case, but in today's political climate in the U.S., I wouldn't be terribly shocked if it went either way. I give it a 60% chance he loses, 30% he wins, and 10% some kind of settlement is reached with the bar. I imagine that even if he loses, there are far nuttier states than Florida that he could still possibly get a law license in.
And I don't think the judge being religious has a thing to do with it. Heck, I'd expect the left to cut a wider berth than the right. A conservative Christian judge might impose his own cookie-cutter version of Christianity on this, thinking that making defamatory remarks is definitely not very Christian, whereas a far-left judge might actually buy Thompson's arguments on some sort of relativistic grounds.