Seems like there are a few separate issues here, and it's tough to piece out exactly what San Diego County's complaint is... but from what I can tell, it seems like the gathering is big enough to fall under some sort of category of "religious assembly" which requires a special permit.
Meaning, there wouldn't have been any problem if it was the same number of people getting together to watch the Chargers, unless they were praying to LT, which doesn't sound unlikely.
Sounds unconstitutional to me, on both grounds of freedom of religion and freedom of assembly, and possibly even equal protection. And, more than that, it's numb-nut f-ing stupid on San Diego's part. Breaking up a local Bible study on Good Friday? Yeah, that's great press--totally worth whatever permit fee they were hoping to wring out of 'em.
