Legal Question in Civil Rights Law in California

"Have church"?

You mean express your Constitutionally protected 1st Amendment right to freedom of religious worship, freedom of speech, and freedom of association, in your home? Yes, that is still 'legal'; for now at least.

IF someone uses their R1 zoned home for a business, commercial or other than residential purposes, which substantially impacts the neighborhood character, traffic and noise, and clearly requires different zoning, then that is a different question. You could not run the massive Crystal Cathedral Sunday services in your living room with 100s of cars clogging the streets. But having friends over for Bible study, prayer or worship services is no different that having a birthday, sports or Tupperware party with guests' cars creating parking congestion. Neighbors have to reasonably accommodate each other with courtesy, both sides. That's called 'civilization'.