I think both the mages and the Templars paths have some credibility issues. With the mages it is that whole time travel thing whilst with the Templars I really don't get why we are being accompanied/supported in our approach by a bunch of Orlesian nobles when the Templar base is in the heart of Ferelden. Did the monarch give us a free pass on that one? Seeing as how much the Hinterlands was suffering from the mage/Templar situation, as opposed to Orlais suffering from their own civil war, I'd have thought the support of Ferelden nobles would have been more appropriate and more likely to have swayed genuinely good Templars. I agree with the reasoning about the differing trust you give to Dorian and Cole in the two runs; it did seem laughable that the moment you make a decision for the mages Dorian magically appears at your door to lend his help, yet has clearly not been hanging out in the vicinity since if you opt for the mages he has to run for his life ahead of Corypheus' forces.
For my male Lavellan, who is himself a hunter, Dorian ascribing what was going on to time magic seemed a bit hard to swallow. He was pretty convinced that what was going on had to do with blood magic mind control, particularly considering who we were dealing with. However, on the face of it, when the mages felt threatened they ran into the arms of Tevinter, so in the words of Shartan "the enemy of my enemy is my friend". There is no love lost between him and the Templar order but given a choice between them and Tevinter, he opts for the Templars. He conscripts them afterwards though since they've lost all their senior officers so it makes sense to him. Ironically of course he ends up romancing a Tevinter mage.
My female mage Lavellan was more sympathetic towards the mages, particularly those who seem to have been given no choice in the matter, and having healthy respect for the magical power of Tevinter, if not the actual inhabitants, is more able to believe Dorian's assertions about time travel. I have to admit that travelling through time with Dorian does make it a lot easier to trust him and shrug your shoulders when he says some of the more objectionable sounding things (to elven ears). She was really quite smitten with him and I kept wondering how long he was going to keep the fact hidden from her that he was gay. When we did his personal quest and everything was revealed this was one time that I was able to say what I felt since when we got back to Skyhold she did give him a mild reproof about leading her on, then put it behind her and suggested they could still be friends. As a result, from that point on (since we had already had all the contentious discussions about slavery and such back in Haven) her time with Dorian was a really positive one and he became a really devoted companion, which was just as well considering what Solas did to her.
I also agree that I wouldn't want Dorian to be an unbelievable goody two shoes. I'd always expected that he'd have a positive view on slavery and use the arguments he did. I just wish the writers had acknowledged that a relationship is a two way thing and that occasionally he'd been allowed to recognise how his words might offend or distress the one he is supposed to care about. I know he has no experience of a proper relationship but he's not stupid and really sometimes its just a matter of common humanity. Why can he talk affectionately about Felix but deride his lover for "sentiment" when they're just trying to show him that they care?