It does appear that the pastor from the OP muddied the waters by going through the process of getting his group made into a church after the city told him that they were going to be treated as a church.
So what about this case?
Home: No place for Bible study
We debated this case on another board, and this is what came of it, in the end:
Bible Group Gets Apology from the County
Reported by: Elex Michaelson
San Diego County has apologized to a pastor and his wife who were cited and told to get a permit for a weekly Bible study session held at their Bonita home.
In a letter dated Wednesday, the county's chief administrative officer Walter Ekard
said the citation should never have been issued and a permit is not required.
Ekard blamed the mistake on "unclear language in the zoning ordinance." He also said the county is taking steps to improve its policies and procedures.
In April, David Jones and his wife Mary were told they could be fined $100 to $1,000 if they didn't comply with county codes that prohibit holding religious assemblies without a major-use permit.