Why is religious conscientious exemption held higher in law (and the answer to this is partly tradition) than philosophical conscientious exemption?
As you said, tradition. Yet where you seem to take the position that religion should be leveled with other philosophies by denying the use of a religious reason to engage in discrimination, I take the complete opposite tack. To me it doesn't matter why that photographer we've been using as an example wants to be an idiot and not shoot gay weddings. When rights conflict, there is a need to choose which takes precedence, but I see no compelling reason in this case to force him to provide that service so as to facilitate a right to be married. To me it's not freedom of religion that rights laws trample but freedom of association. Freedom of religion is but a specific case of freedom of association. I grant the OP posed the question in terms of that specific case, but the right that is trampled is the more generic one.
No he's not but you've just proven you're against the first amendment by comparing freedom of religion to segregation. What's so bad about freedom of religion which includes the church's right to not accept gay marriage? Does this mean you're against freedom of speech as protected by our first amendment too? You must oppose it because you're sure against people speaking from religious grounds to support where they stand.
Which, by the way, was an argument many people made in the 1960s and 70s and even into the 80s - that God himself disapproved of mixing of the races (citing various vague Biblical references along with Biblical endorsements of slavery and related), and that their Christian beliefs prevented them from serving black people alongside white, or of catering to mixed-race couples.
