"1st amendment. Seems to me, but strangling the size of a church, a government could indeed persecute a religion."
It's not strangling a religion. It's asking a mega-church to build in an area that will support the traffic, noise, etc.
Would you feel the same if the local mosque would build a 1000-person building at the end of your street? Would you support their right to have a big building, AND broadcast the calls to prayer via loudspeaker?
Today, churches aren't even allowed to ring church bells on Sunday. Which was traditional. At least around here.
I live near four churches that could be considered no less than monstrous. I have never heard any noise from these churches, even on Sunday. I'm more concerned with a municipality saying to a church that what size it can be allowed to grow.