The two questions are:
Should communities have the right to enact and enforce zoning laws?
Should houses or places of religious worship be exempt from zoning laws?
To the first question I think zoning laws are necessary. If an intrusive business, say a manure processor, opened up a business in a residential area it directly affects not only the quality of life but the value of poperty.
To the second question, it is more complicated. If a person wants to get together with 10-12 people in their own home to pray, it should be exempt. As long as it doesn't become a nuisance. Based on what the guy wants to do with his property in this instance, with the numbers of people, megaphones, etc he should not be allowed. He can open a church anywhere in an appropriately zoned area if he chooses.
I moved my business and now work out of my home. In Vermont anyone can have a home based business regarless of zoning as long as they meet certain criteria, like they can't have any employees, they can't have a sign visible from the street, they can't use more than a certain amount of street parking for their customers.