The First Amendment doesn't just apply to Congress, it applies to all branches of the government.
I'm so surprised people are having a hard time understanding that if you have a government job, you can't enforce your own beliefs on other people through that job. What if the head of a state liquor board changed his religion to Islam, and suddenly decided to deny every application for renewal of liquor licenses, because alcohol was evil? What if whoever it is who grants pistol permits decided, "I'm a Quaker now. Guns are violent, I'm a pacifist. No one gets gun permits any more." What if 51% of your local population were Muslim - a strong enough majority to guarantee to get a Muslim elected as Mayor or whoever it is in your city who grants permits for public festivals, and festivals at churches. "Nope, we're not granting you a permit, because there's going to be music." "Nope, we're not granting you a permit, because there's going to be alcohol."
You seem to think it takes a law to deny people the right to do something, and you seem to agree that it would be wrong to make a law to enforce a religious belief that was central to only some religions. Or, are you in favor of Sharia law in your town if a few Muslims are elected to your town board/city council, or whatever local legislative body you have? You seem to not realize that individuals and groups can still abuse (illegally) their government position to oppress people of other groups. And, that's about as wrong of a position to have in this country that you could have. "I'm the county clerk, and I refuse to certify this home sale, because it's to a Muslim/Hebrew/black/gay/etc."