I don't share the reflexive opposition to any and all conscience exemptions that many other LGBT people have, but it's been established since Reynolds v. United States in the late nineteenth century that the First Amendment protects all religious belief but not all religiously motivated behavior.
I think the Court could conceivably rule against anti-discrimination laws as a whole using freedom of association. A decision like
Boy Scouts of America could turn into something along the lines of overturning
Obergefell, but it would have to extend to state governments, at least in certain exceptional cases.
Indeed, the “suspect classification” could very easily be thrown out altogether as definitive use by Roberts and Kavanaugh.