Yes, the restaurant's decision is problematic for me. I could make an argument that they aren't discriminating against people with Christian identities, because Christians hold diverse beliefs about abortion and LGBTQ people.
I could argue that the group is so odious that public accommodation laws should be excepted in this case, and probably not applicable since identity questions are not raised.
But I find such arguments strained and hard to advance with a straight face.
I admire the restaurant owners' principles and I appreciate their allyship. But I don't think denying public accommodation should be part of the American experience.