The nature of almost all religion is inherently discriminatory.
And that is okay.
Why? Why are churches allowed to violate the law, but all other public accommodations must submit? And don't say freedom of religion. The first amendments protects that from laws targeting religious practice, it doesn't give them a free pass to ignore the law.
It is essentially the same reason why States can't legally ban gay marriages.
In order to deny anyone a protected right, the State(meaning either States or the Federal government) must demonstrate that there is some compelling state interest in denying those rights.
There is no compelling state interest in forcing churches to violate their internal doctrines by requiring for example the Catholic Church to marry Jews.
However, the State would have a compelling interest in preventing churches from practicing human sacrifice.
Ok, so why is there a "compelling interest" to force a baker to bake them cakes, but not a priest to marry them?
Sigh you still have this backwards.
The state can only deny rights when the state can demonstrate a compelling interest in denying rights.
The priest is protected by the First Amendment from being forced to practice his religion in ways that violate church doctrine.
The baker baking cakes can make the claim of religious exemption, but State does have a compelling interest in requiring public business's to business's even with 'despised minorities'- that was established in the 1964 Civil Rights Act.
Why is it not a compelling interest in both cases? Isn't the actual marriage more fundamental than the cake?