This assumes that only churches/places of worship have freedom of religion. This is clearly not the case, as the supreme court ruled. A completely secular business can be own/run by religious people, and forcing them to violate their religious beliefs is a violation of their constitutional rights.
This is clearly not the same as the situation you are referring to. They register and receive government funds as a secular university. They should be held to the same standards as any secular university.
Also, what they are doing know is pure discrimination after the court ruled.