This is a question that concerns American society.
It assumes that, in a disputed incident, politics or courts provide the answer. However, perhaps it would be helpful to refer to the United States Constitution (Amendment I), the one document by which all Americans and America, agree to live.
Amendment I begins: “Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof…” Religious liberty, the “first freedom,” must have enjoyed the special esteem and attention of the American founders — otherwise, why would it have been listed first among the enumerated freedoms?
The constitutional amendment on religious liberty demands Congress back off from civil society — so as not to impose an established religion on the nation at large, and so as not to oppose religion from being practiced in the general society. Therefore, religious liberty, according to the Constitution, really does make it possible for Americans to practice their religion in (relative, not absolute) freedom.
“Free market capitalism” is about buying and selling. In American society, buying and selling should be done by the buyer, and the seller, in good conscience. That is, the buyer and the seller should be able to enjoy the freedom of religion in their buying and selling.
If they discover a disagreement on the way to an exchange — in which one cannot buy for reasons of religion and/or one cannot sell for reasons of religion — then they move on to the next potential transaction with another. The state need not force a transaction that would violate the conscience of one or both.
So, yes, in the abstract, I would answer that religious liberty trumps free market capitalism. If it does not, government has to enter this arena and act as an umpire. Unfortunately, government’s umpiring skills are not exceedingly nuanced.