"It's time travel, go with it," is the response of a sceptical Inquisitor to being told by Dorian the reason everything in Redcliffe seems so weird. May be the writers were being rather self aware with that line but it breaks immersion for me.
The difficulty I have with the whole Hushed Whispers quest is that if I am keeping in character then I turned up at the inn, Fiona starts acting weird, we discover she has indentured herself and all the other mages to a Tevinter Magister, from a nation where we know that blood magic manipulation is endemic and then another guy, also from Tevinter, asks me to believe him when he says it is all due to time magic, something that the rest of the mages present have no knowledge of or consider possible. I then go away to think through what I have seen. In all honesty would I be willing to place my trust in some person I don't know from Adam, just because he has a pretty face, to help me infiltrate a castle where the Magister likely has control over hundreds of mages to turn against me. Why would anyone think that is a good idea? The fact that it turns out to be ridiculously easy to do this, does not take away from the suicidal risk you would think you were taking.
As for the suggestion that Alexius was simply trying to go back to the wrong point in time; so far as I can understand it, Corypheus doesn't just want to go back and kill the Inquisitor, he wants to get the anchor back. To do that you have to go back to before the explosion. Then Corypheus will have both bits to his set, can unlock the orb and walk into the Fade using the anchor. Alexius doesn't stop trying to do this once the Inquisitor disappears into the ether because the anchor went with them. So he keeps trying to turn back time to the point that Corypheus demands, getting increasingly desperate about it as his diary entries show.