I don't know the history of the inclusion of that particular provision, but I suspect it was based on a vision of a robust protection for freedom of religion and a recognition that there were potential risks of a chill in that ability to practice if we were seen to criminalize certain kinds of speech.
However, at the same time, if that is used as a safeguard or as a mechanism to engage in hateful conduct, then surely we have to consider how to address that kind of conduct so that religion doesn't provide a sort of a blank to allow people to say anything, especially when it creates some of these kinds of harms.