I get attacked the second I go down there (I'm a priest), should I just fight on?

Yes keep on fighting a few levels down through the paladins.

I found him, and talked to him, but he was still hostile after the conversation. Is there a way to turn that off? I had to order my men to stop attacking and retreat through the portal

He did not attack me, he was red until he talked to me and then he and all his men immediately became 'blue' so I don't know.
I did not accept Jean's request to present the evidence to the high inquisitor, but to investigate myself. I', not sure if that has something to do with it but I would doubt it.
The only thing I can think of is to reload and press F before you go down and make a straight beeline for the Grand Master.

WHAT citadel? !@#!@@&#@!

Walkthrough and elsewhere "the citadel" is referred to, BUT what and where is this "citadel?"

The World Map has Citadel Surroundings but walkthrough implies a "second floor" which is NOT applicable.

There should be a location called "Citadel" on the World Map - a bit to the north from the location of "Citadel Surroundings". It should become available after you talk to Jean de Guise in NW Alvaron.