I read this article over at NPR this morning. Perhaps you have head of it. It involves a Lutheran school teacher who was asked to resign and was then fired essentially for having narcolepsy. The teacher sued for discrimination and the case eventually made it to the Supreme Court. The court ruled in favor of the school on the grounds that she was a minister was therefor not protected by anti-discrimination laws.
I think this ministerial exception to anti discrimination laws could be argued both ways. For example, if a person was a fully qualified, say, Lutheran minister working for a church, and at some point that person lost their faith but continued to perform his or her duties as a church leader as well as anyone else, should that person be let go? I would have to say no, but I could see how someone could make the case that the minister should be fired.
What I find disturbing about this case, however, is how loose and fast religious organizations are allowed to play with this power. This is not a case of a rogue minister trying to convert the kiddies to devil worshippers or worse (gasp!) atheists. This is a case of an employee who got fired for a disability, and the reason given was that she led the kids in prayer and therefore the law could not prevent the church from discriminating against her on account of her disability. I wonder (I really don't know) do any other organizations have this option? Or is it just for the religious?
I really don't know whether to be enraged by this church stomping on its employee's rights or whether I should be experiencing schadenfreude and saying, "That's what you get." Regardless, I shouldn't feel surprised.