Bakery is of course in the right and has authority to refuse service to anyone they see fit. Just goes to show you that this kind of shit works both ways.
If we want to keep have these investigations into discrimination of places of business, just know that this is on the other end of that discrimination spectrum, and will have equal justification in the eyes of law. Anything else would be, of course, discrimination.
Is that really what people want? Everyone can be spun a bigot in some way, under the auspices of law, and this is kind of proof of that.
On another note, this is why religious protection laws are stupid. If we just agreed that independent entities can make their own decisions about who they do business with, we wouldn't need religious protection clauses that cause more trouble than good. We're in pretty deep into this rabbit hole and anti-discrimination laws, and I'm generally not a fan.