Earlier quoted context omitted.
I agree that that headline is awfully dramatic --- but your summary misses what is, to me, the most interesting part of the article: that enforcing freedom of religion has led to inconsistencies in the way we maintain those other rights. The fact that we do have explicit protections of the freedom of religion means we are failing to genuinely protect speech, association, etc. That seems like a conclusion worthy of at…
I absolutely agree with that premise. However, I'd only buy that as the writer's real message if he wasn't going for a subtext of Gee, look at all the unreasonable privileges people get on the grounds of religion! I'm reminded of the argument that we shouldn't support gay marriage, but instead should support getting government entirely out of marriage and letting any consenting adults form any arrangement they want.…
That says something about your powers of observation.
I note that most people giving that objection are unmarried, and a large fraction are "uncoupled".