Most people are born into their religion, as a matter of culture. Frequently, religion is integral to their culture, and even if they do choose to leave that religion, it likely will leave an indelible mark- good or bad-
Their purpose is to other-ize religious scientists, exactly like what the yellow star was used to do to Jews by Nazis, (and at other times and places.) I think we all know what Nazis did to those they otherized.
The rhetoric is absolutely the same kind of justification for forcing it is also the same. When non-Jewish Germans started sympathies with Jews, do you think they admitted it was to encourage discrimination and bigotry, or do you think they said things like “we know it’s difficult, but they do shoddy work and you should know that you need to keep an eye on them.”
Couching it in the rhetoric of atheist enlightenment doesn’t make it okay. It’s still bigotry, and while the OC might not realize that, meaning to or not, it’s still advancing bigotry.