Religious persecution, or overbearing regulations?

This has everything to do with the use and the county is trying to establish what the house is being used for.

Here is the link to the San Diego code of ordinance.
http://www.sdcounty.ca.gov/dplu/zoning/z2000.pdf

Religious assembly IS allowed in in single family residential area., but "with the issuance of a Major Use Permit". And the ordinance specifically says "religious assembly" and not church.

And how many prayer meetings are being held a day/week/month? If it's happening 1x a day, I'd say the people living in the neighborhood have a legitimate beef.