I mentioned this on the EM forums once, but it made sense to me about how to view the Amarrian faith. The best concept I had of the Amarrian faith was a cult, very loosely based on Judeo-Christian ideology and symbology, who voluntarily left for the frontier to create their own "pure" society. Think the Pilgrims of North America, or the various migrations of sects over the world who left their home, or, perhaps more telling, Jim Jones setting up a colony in South America.
It's quite likely that that the proto-Amarrian faith was vastly different from "mainstream" catholic(little-c)/Christianity/whatever, even at that time. Mainstream, orthodox religions don't pack up and go form their own communities in the frontier, thats typically the actions of the unorthodox, the radical, or the just plan nutty.
Thinking of the Amarrian faith as a Jim Jones-esque religious colony that was cut off from Earth society, survived, refined its doctrine and expanded and created an Empire conceptually make sense to me, as well as making them quite scary.