Religion is protected here, but not above American laws, which are made by men.
The First Amendment begins…
“Congress* shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof…”
* And by incorporation under the Fourteenth Amendment, all government legislative bodies, courts, and other policymaking agencies.
You are arguing that government has the right to make laws that violate the free practice of religion, and that those laws take precedence over freedom of religion. The First Amendment very clearly says otherwise. Freedom of religion takes precedence over any laws which government might make that are in conflict with it. The same holds for freedom of expression, and the right to peaceably assemble, which are also explicitly affirmed in the First Amendment, as well as freedoms of conscience and association which are strongly implied therein.