Well, Religious Freedom of beliefs do not take precedent over gender identity, sexual orientation, etc.
For example, when I worked at the Municipality in Halifax, certain religious groups couldn't show skin in front of a male.. but we would have people working the swim lanes that were trans. So what do you do in that case? Well, since a trans person is who they identify as, they are female and we would not pull them from working there, that shift etc.
Frankly, any person who's religion has tenants in it that actively discriminate against another human being, for who they are, should probably take a good long thoughtful look on whether they would want to worship a god that would prescribe such a thing.. but hey, that's easy for me to say as an Agnostic and doesn't believe in 'the word of god' written by a bunch of dudes thousands of years ago that is unable to reference a large quantity of the earth's history that had other living creatures (e.g. Dinosaurs) ruling the earth.