Looking at this as just a political structure question and without implying any moral judgement (all politics is essentially moral judgement enforced by the state) the only counter measure that would work at this late stage would be an amendment to the legal codes of states and municipalities, perhaps backed up by a federal constitutional amendment, that guaranteed the right of the citizen to conduct his or her business according to his or her moral values, regardless of any other laws.
This could be given specific language on sexual orientation and gender issues, and worded so that similar actions might not be legally taken to discriminate against identifiable racial or religious groups. Or we could go full-libertarian and discriminate on any basis the individual chose.
I am not willing to concede the point that discrimination against sexual orientation is equal to racial discrimination, whether it is in legal codes or whatever, that remains a moral judgement and one likely to be based on religious beliefs. The state has already de facto taken the position of overturning religious belief on this issue and that seems overtly unconstitutional. A test case is needed, either this one, or the Portland wedding cake case, at the highest court level, and then political action is required to make the law conform to belief if that is not the outcome achieved.
People may think that this is a minor issue that is limited to a few cases, but over time this issue can explode into society-wide tests of belief on these issues and people of faith will find themselves unemployable and out of work in more and more sectors. For example, it could soon become normal practice to test all sorts of categories of employment for beliefs about sexual orientation, climate change, maybe even whether or not you believe Russia tampered with the election. Why not? Once this thought process jumps the shark, we are basically on the wrong side of the shark for good with no legal recourse.
I think it is coming to that - you will be required to declare “loyalty” or agreement to a list of politically correct things. It will be the modern equivalent of being forced to worship the Emperor as a god.
I wouldn't even go that far. These people don't discriminate against homosexuals. You could go to their stand and declare your homosexuality, and they would still sell you pumpkins, blueberries, apples,etc. They just won't rent their farm for homosexual marriages.