I think you're generalizing waaay too much. Remember how Catholicism and Christianity in general ended up with the Christmas tree, Easter eggs, and so on. Sure, there would be sects that would insist that there's still no such thing as aliens and therefore all of these "aliens" must be demons. But most would adapt to meet reality to whatever extent they would need to to survive. The Roman Catholic Church would have Andorians believing that Jesus came for them, too. The Abrahamic religions are sort of henotheistic at their core. In my opinion, that's part of why people (Jews and Christians, at least) like to bring back those little containers with a bit of the soil from the Holy Land when they go to Israel. All it would take is for a reasonable Imam to issue a fatwa that says that when they're away from Earth, Muslims can bow toward a soil sample *from* Mecca rather than toward Mecca itself. The difficulty would honestly not be imagining the ways that Islam would have to evolve to fit into the Federation. The difficulty would be that current *real world* fundamentalist Islamists would decide that doing so was somehow an insult to Islam and attack the production. True. And being Egyptian (if I recall correctly), they very well could have been Muslim. Unlike some rather disgusting ideas put forward by POTUS candidates this election season, I doubt the Federation makes them wear badges or other indicators.