They'll lose in the Supreme Court. It's a clear first amendment violation.
I don't think so. A church's land use can be regulated as long as the regulation is reasonable and non-discriminatory. For instance, if this guy was raising rattlesnakes for
"snake handling", no one would have a First Amendment problem with stopping him.
But that would be because it is probably illegal to raise rattlesnakes privately, or expose children to them, etc.
In this guy's case, he would almost certainly win, but it's a moot point now because of the disposition of the case.