Admittedly, it's a very different concept, but the situation reminds me of bona fide occupational qualifications. Basically, it answers the question of how much is discrimination essential to your business model and to what extent we must tolerate it. With the halal butcher shop and the Indian restaurant the answer is: yes, it is essential. (Well, not discrimination, but their product is very specific.) There are well established definitions of what constitutes "halal" and there's a pretty solid understanding of what Indian food is. But BFOQs aren't infinite in scope, they're actually pretty limited. Hooters is still fighting over whether or not it's legal for them to discriminate against male waiters.
Like I said, I have little knowledge of the specifics of the cake issue. But I don't see the big difference between that and the Kim Davis thing. Like yeah, marriage itself is more important than cakes. But still, the solution to getting a marriage license in her county is as simple as going one county over. Many other counties were issuing marriage licenses. A half hour drive would've solved their problem. But the bigger issue is that people are flouting the law to make a personal statement. That shouldn't be tolerated any more than if I cut off the fire escapes on my building and claimed first amendment protection for it.
The difference is that Kim Davis was an elected public official, whose only job is to uphold the law to the letter. The baker was a private citizen. Because we cannot fire Kim Davis, her failing to do her job is abdication of her duties, and actually illegal in and of itself.
A private citizen running a private business such as a Christian bakery (which is exactly how he advertised himself) is way different. He has not been elected.