Our traditional religions were formed in worlds that seemed to their inhabitants "enchanted," that is, imbued with spirits who controlled people's lives. The Christian theology of the Spirit reflects the same idea, namely that our lives are conditioned by spirits. 
We no longer live in a world that takes religious spirits for granted. The people who wrote the gospels knew nothing about the universe, the subatomic verse, or even genetics and human fertility. Their time-conditioned ideas about these and many other questions often make little or no sense. Neither do the institutions that preserve them.
I'm personally not interested in religious freedom that preserves pre-medieval ideas about a world we understand much better than the evangelists did. I think religions should be required to defend any of their ideas that have the potential to impact people negatively and, if those ideas prove unsubstantiated and harmful, the religion should be limited, as has happened many times in history