Religious persecution, or overbearing regulations?

Of course there is a Constitutional dilemma. You have a conflict here between freedom of religions/freedom of assembly and a city ordinance that restricts one or both of those rights. You might think that the issue should be resolved in favor of the city, but the dilemma is still there. There are questions here regarding whether this is a reasonable restriction of freedom of assembly and there will also be questions on if the city ordinance is unconstitutionally vague, meaning that it is so unclear that it violated the notice requirement of Due Process.
You have the freedom to get the proper permit. This is a situation that has nothing to do with religion. The only issue here is human bodies and vehicles and their effect on the immediate environment.