My depiction would involve humanity becoming more cultural relativists. Not necessarily a homogenizing of beliefs but rather an acceptance of the differences in each other. I would depict this on a religious level as well. I had a hijab wearing Muslim in mind for a "should have been" Enterprise series. Of perhaps have a Chrislam crew member.
Religion isn't just a headcloth or piece of jewellery, it's a doctrine you are required to live by, and an organisation which has moral authority over you. So I don't see how the Federation could reconcile religion with universal human rights, i.e. equal rights for women, no homophobia, no child abuse, no restrictions on harmless private behaviour.
There's also the problem of religions being Earth/human-centric - if humans are God's special creation, where does that leave all the alien species? Can we just kill them like any other animal?