We've had these discussions before, and I'm certainly not going to defend government discrimination. All 3 of the cases you mentioned deal with how the government treats people and prohibits them from some arbitrary distinction under the law. I think there's something to be said about looking at the framer's intent with the 2nd amendment and realizing that they clearly intended an individual right to bear arms versus the "regulated militia" aspect the 4 justices came up with in their dissent in Heller. True, when the 14th amendment was passed, Congress certainly didn't have homosexuality or interracial marriage in mind. But they did establish an ideal in liberty, and the justices rightfully followed that ideals concepts in ruling in Brown, Loving and Lawrence.
Kim Davis was wrong because she was a representative of the government and her personal opinions or beliefs don't allow her to discriminate in a legal capacity. Frank the baker, who isn't funded by taxes and can go belly up at any moment, shouldn't have to sell or associate with anyone he doesn't want to. You and I can both think he's an asshole and refuse to provide him with our business. SCOTUS ruled in NAACP v. Alabama that the freedom of association was inherent in the first amendment. I believe constitutional liberties take priority over hurt feelings.
Then why put language about militia into the second amendment if it isn't an amendment about the basis for state militias? I'm not asking to argue or pick a fight...it just seems odd. And if we're to look to originalism as our model, surely we have to ask at what point that no longer applies. The framers could not have intended for people to have the weapons they do, today. I'm not saying that they would or would not approve..I'm saying we cannot know. Originalists and textualists love to say that you cannot judicially legislate beyond the scope of the Constitution or the framers' intents, but that's exactly what happened with gun rights. We assumed that a bunch of men who wrote something 200+ years ago, when the weapons of they day were single shot and could only be used to mass murder when fired by many men at once, would believe the same thing today in the modern context. They may. They may not. We cannot know. But I'm okay with that, because the Constitution is vague and must be applied as best it can to constantly changing issues.
I also agree that liberty trumps hurt feelings. I'm not against commercial bigotry because of hurt feelings, but because of another Constitutional principle which is equality. We cannot have anything close to an equal society if basic commerce is denied to certain groups of people. Frank the baker doesn't matter. What matters is the idea that one baker represents not only all bakers but all commercial enterprises, such that if Frank can legally discriminate so can all businesses. As the NAACP is a private membership organization, the rules are different, much as they would be for an all-male golf club or all-female college.