It will be very different because the Imperial Chantry is kind of run by the state in a sense. The Orlesian Chantry is over the Circle (or was) and is pretty autonomous... or as autonomous as an international group can get.
The Imperial Chantry is... well, stuck in a single nation that is run by the Imperial Circle. The Circles are the political parties and all the people in power, secular and religious, are pulled from the Circles.
The Imperial Chantry isn't as free to do as it will (compared to southern Chantry) since it is limited to being at the mercy of a single nation and the Circle. If the southern nations open the door to other Andrastian faiths, and the IC is able to gain ground in Nevarra, I think it would do a lot better and be in a better position to be more anti-blood magic or anti-slavery or at least more free to discuss ideas.
Then again, I get really biased and optimistic on matters of the Chantries. While I prefer the Chantry with Viv as Divine, I'm starting to prefer the Imperial Chantry since it doesn't have the issue of possibly getting its dogmas thrown out the window because of the Divine's feelings about them (Lel...).
Please, please have the IC go to Nevarra, it would as great as Tevinter! (If not better...)
Nevarra+Tevinter