Well, not necessarily just "organized" religions operating businesses.
Let's keep it more direct for a moment. As in my business is in Christian materials. However, I'm not a Church or faith. Just a Christian businessman. So, I have a private and independent business that produces, I don't know, study guides to the Bible. Or, I run a Christian dating site. Or children's books that are Christian child friendly. You get the idea. Employment and benefits issues based on sexual orientation.
Now I provide a more general service. I plan weddings. Now a gay couple wants me to plan theirs. "I'm sorry," I say, "but to me marriage is a sacrament between a man and a woman. I absolutely can not have any participation. However, there's two other planners nearby." They ask if I'm refusing, and I say yes. Denial of service based on sexual orientation.
You already touched upon Catholic schools. They shouldn't be able to actually operate like they mean that "stuff."
Sure, they can say those pretty prayers and bow their heads. But to live it? Only in the home or directly under the roof of the actual church building.
Freedom of orifice selection.
Freedom of religion...in the home and the Church building.
Freedom of association.
Freedom of speech.