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The Knapps will have to reorganize as a non-profit religious institution if they want the Constitutional protections afforded churches and ministers.

Ever heard of a little case called Hobby Lobby v. Burwell? That held that even a for-profit corporation could refuse to abide by certain laws that were in conflict with the owners sincerely held religions belief. Under RFRA, the law has to address a compelling government interest, and it must do so in the manner that least affects the company's religious freedom before the company can be forced to comply. Since there are many other places gays can get married in Idaho, forcing this particular facility to marry them, against the sincerely held beliefs of the owners, is not the solution that interferes the least with the owner's religious freedom.

I'm not a lawyer (obviously), but the Knapps may run afoul of a “public accommodations” interpretation of their for-profit business. If, for example, Hobby Lobby tried to prohibit non-Christians from shopping in their stores because of the owners’deeply held religious beliefs, I suspect this would be held unreasonable.