Aside what Lou said, I think Gaven is quite right when he points out that Roman Catholic Christianity has a lot of things not in common with the Amarr and that the Byzantine Orthodoxy of the medieval time within the frame of the Byzantine Emopire is a better model in those cases. Yes, the Pope ruled over a state of his own (and still does so), but that has been a differnt state than the great monarchies of the time. How more obvious could it be that here one and the other are not the same, while still being tied to one another?
The fact is that the Pope didn't establish his power from within the European states, nor was he the sole ruler of an European empire: He established his power against the Kings and Emperor's of Europe. There are clearly distinguishable spheres of authority, spheres that were contested time and again, but which were defended by the 'worldly' as well as the 'religious' authorities against one another. This was the basis for the development of a secular state and the seperation of state and church:
A basis that Roman Catholicism had to live most of it's existence with and which shaped it quite a lot. Such a basis is entirely absent in the Amarr Empire. I'd not go as far and say that Holders are clergy, but they have a religious function. We're so much shaped to think in the terms of seperate entities when we think of church (religion) and state, that it's not easy to comprehend that in Amarr these are apparently not, by any stretch, seperate entities. Or how someone can have religious functions without being clergy, apparently.
So, while I agree that Amarr clerical titulature apparently borrows a lot from catholicism (or orthodoxy, as the titles aren't that diferent, basically) and that this implies a certain similarity in the function of those that hold these titles, this by no means implies that the organization of Amarrian churches is Roman Catholic entirely. It's rather Byzantine Orthodox in just as many respects as it is Roman Catholic, really. There are also a lot of other real historical religions/states it is resembling in one respect or the other and some of those share as many similarities as RC and BO.
While I personally think that ruling out Roman Catholicism as a model entirely would be bad, I think it'd be even worse to base everything on it flatly, just because it doesn't do justice to how the Amarr Empire (and thus Amarr religion) work. Also, it comes to what Lyn said: If you do justice to Amarr by taking inspiration where it's appropriate to take and thus take inspiration from many different sources, it's far less easy for the trolls to troll as Lou explicated so pointedly.