Obama has called homosexual marriage a "civil right" which sets the table for lawsuits under the Civil Rights Act, from which the churches' nonprofit religious status will not protect them.
Then, a next step is for a conservative president to refuse to renew the Civil Rights Act, which comes up for renewal periodically.
Regardless, no mere policy of a church is going to stop a fascist government from doing whatever it whats. That’s a fool’s errand.