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Except that religious tolerance, including tolerance for religious organization's religiously grounded specific discrimination stances, is specifically enshrined in the Constitution. Businesses have no similar or even remotely analogous protection.

Drawing an analogy between an organized religious organization like a Church and a business like a restaurant is a fundamental misunderstanding of the law. This specific dividing line has been held up over and over again in cases where religious organizations incorporate a business entity, and then wish to push particular discrimination policies specific to their practices into that business.

A White Supremacist church is free to be discriminatory, but the bakery it owns and runs as a separate business entity is not for example.

However, IIR, a religiously owned organization, like a corporation, may choose to discriminate based on religion. So the White Supremacist Church's bakery, let's say it's Lutheran, may choose not to hire non-Lutherans at its bakery. This was actually held up by SCOTUS in a 1987 decision for a Mormon church owned corporation.

edit http://www.ecfa.org/Content/TopicReligiousDiscrim