Hmm, I'm sorry to hear that. My own faction being ignored entirely and damn near blocked out of the developments is one thing if at least what's being done benefits others. Of course, I disagree with the notion that the Amarr Empire shouldn't be portrayed as religious-fanatic-nutbags, because that's exactly what I've seen since my first days in the game, both from the PF and the players. The IGS and in-game channels have pretty much had only that from the Amarr side, if you're not on the inside yourself, so the WH40K portrayal from the actors seem very consistent with what the players themselves portray in public.
As for quick change in the Empire, that's just the unfortunate reality of this being a game manifesting. We don't actually have several centuries of real time to see changes happen in this game, so (necessary) changes will unfortunately have to be somewhat abrupt.
I think you're a bit quick to throw out "one-sided view of the Amarr", though. That there'll be difference in opinion how factions are portrayed and how they should be portrayed happens for all four and the outlaws. I'm a little more of the opinion that you can't really have it both ways. Amarr are very much based on theocracy, religion, zealotry and so on, which makes it a bit odd if you're also going to ignore the downsides of this kind of society. The Caldari have the downsides of hyper-capitalism down pat, and the Fed has the obvious issues their hyper-"freedom" brings down upon them. There needs to be balance in how these societies are portrayed and all four needs to pay the price for their particular fields of "excellence".
For the hyper-religious Empire, that means zealotry, religious fanaticism and so on. That's pretty much exactly what we get from the players already, so I can't fault the actors for consistency.
Besides, given how utterly stupid they've portrayed officials from the other factions, I'm not entirely sure what else could be expected.