Anti-discrimination employment law seems to be geared towards preventing institutional discrimination against marginalised groups, rather than preventing individuals from exercising their personal preferences. I don't think it makes a lot of sense to view it as legislation that helps negotiate peace between warring factions of equal status.
I think -- correct me if I'm wrong -- that outside of anti-discrimination law there's also a commonly-held notion of voluntary toleration. Being an intolerant person seems to be held to be a bad thing, within certain bounds. We frown on some kinds of intolerant personal preferences -- if I refused to ride in an elevator with foreigners, you might think I was pretty creepy. (But what if I refused to ride in an elevator with people who refused to ride in elevators with foreigners?)
Let's say you are interviewing a candidate for a job. In casual conversation, the candidate mentions that he is a member of a rather old and prestigious country club. You've never heard the name of the club before.
You look up the country club afterwards, and are surprised by what you read. The club refuses membership to homosexuals. It revokes the membership of couples who use birth control. Leadership positions are reserved to unmarried males.
The candidate is otherwise competent. Under what conditions would you hire him? Would you want a law passed banning hiring discrimination based on country club membership?
(The country club is analogous to a nicer version of the Catholic church. I left out a couple bad things.)
Religious discrimination is illegal in many parts of the world, and I think that's probably a good thing. Still, keeping this at the object level (no meta-rules or veils of ignorance) it seems to me that discriminating against religious people is fine. I'm curious what other people think.