You appear to be saying that religious beliefs can be protected only if it's a widely held belief with a long history. Why does philosophy, western tradition, or what you think about its intrinsic evil matter to the JW who holds that belief? Religious beliefs are religious beliefs. Are only the majority to be protected? Freedoms are supposed to protect the minorities as well. And I doubt religious freedom laws mention philosophers and western traditions.
I'm not exactly sure how to answer your question, but I do think that the following points are worth noting:
If you tell the Jehovah's witness that, if he takes a certain job, he must administer blood transfusions, then you are inconveniencing a member of a tiny, insignificant very modern cult. [Note, of course, that I am not speaking in this way simply insofar as I am a Christian, Catholic, or anything else. This is just true. There's roughly 8 million of them. They were founded in the 1870s. I don't think that anyone who is even vaguely familiar with the sect would deny that they are, in at least some real sense of the word, a cult.] And you are only inconveniencing members of said tiny cult.
I can't think of anyone else who has a religious objection to this, or even a general moral objection to this. The JW are literally, as far as I am aware, the only people who would object. A tiny sect with an average membership, even recently, of roughly 8 million people, a tiny sect who believe nonsense that nobody before the 1870 believed.
And you know what? You probably aren't inconveniencing the JW that much. Chances are, he wouldn't want to be in those fields anyway.
If, however, you say: "You must formally cooperate with a gay 'marriage,'" you have literally just alienated the entire western tradition and not just the Judeo-Christian tradition, either.
I don't know how to express this in first amendment terms. But there is a real difference that nobody seems to care about or be talking about.