to put it another way, judging somebody based on their religious views isn't being prejudiced, because it's based on experience.
what does it mean to be prejudiced? it means you're pre-judging somebody, that is assuming that somebody is a specific way without evidence to uphold it.
so, saying that black men are good runners would be a prejudiced statement. while statistically true, there are lots of black men that can't run worth shit. if you were to judge how fast somebody could run based on their skin colour, you'd be operating in the realm of pseudo-science. even if statistical mechanics gives you a positive answer...
but, stating something about the views of a religious person, as they exist in front of you, is not prejudiced. rather, it is built on the experience of communicating with the person in front of you, as well as perhaps in doing some research into the topic. generally, this is actually going to be an informed statement about the person that comes from judging them from experience, rather than without it.
i'm opposed to prejudice, but i'm not a christian. i'll judge you all i fucking want, but i will do so based on experience, like i ought to. and, you can judge me, too - i'll just tell you to fuck off. the point is that, so long as the judgement is informed rather than uninformed, i see little problem with the actual judging.
i would like to see more judging done, in this matter.
what people believe does matter, and a lot of people should be called out for their oppressive religious beliefs, whether that means firing them or whatever else.