No. If the government begins to regulate houses-of-worship, that only opens Pandora's Box for those religious institutions to turn around and say, "Since we are now being formally taxed and regulated by the federal government, then that gives us the inherent right to dictate that the federal government must honor our [']sincerely-held['] beliefs."

Such an unprecedented move (by the federal government) would also probably get unanimously thrown out by the U.S. Supreme Court.