oh, that's just cruel, i love it 
Oddly enough having an Inquisitor who looks just like Regalyan makes the romance better. It certainly provides a little more explanation why she's not entirely comfortable with the idea of the Inquisitor courting her at first, and why she brings up her past during the romance scene, at least on a meta level.
But still, that would be a pretty big shock for Cass to find that her old flame (or someone who looks very similar) might be behind the Conclave's destruction.
Even then I think that relies on who you put in charge. Cassandra is a lot more likely to take a hands off approach then rule by force like Lei and Viv would. Especially Viv. And remember this is the Middle Ages the Office of the Pope, in the real world, was VERY powerful. The Divine's death in the beginning of the game caused the whole world to run around sqauwking.
It might just be me, but I feel that the office of Divine is the best place to put Vivienne. I don't trust her, but on the Sunburst Throne she's in a highly visible position. Remember, the only reason she didn't get ousted after her election is because of the Inquisition and we've most likely have a list of her opponents and enough secrets and allies to topple her should her gratitude start to wane. She's not going to go Borgia on our watch.
Besides, I highly doubt that Cassandra would let Vivienne do anything that would sully the Chantry's good name, and given her reputation I don't think anyone would argue with her.