I found the ultimate outcome of either side's support to be a very interesting and different way of showing players that their decision on whom to support may not always be vindicated, especially after choosing your final side in the battle for Kirkwall. Yes, Meredith may be insane, power-hungry and corrupted, taking the Templars to an absurd overreach of their station, BUT she was right about the mages the whole time, since Blood Magic is widespread in the circle, and Orsino himself is a blood mage also. Even if it could be spun as that the mages were practicing Blood Magic to resist Meredith's insanity and repression, demonic possession and corruption -and all the chaos and destruction surrounding that- still occurs, no matter what their original motives were.
I think that the point that BioWare was trying to make here is that both sides were in the wrong, and that no matter who Hawke eventually allied with, it feels like you made the wrong choice. I think it's a fresh and innovative way of showing players that just because they have a story and choices that are unique to them, that does not automatically mean that the story will have an ending where their choices feel vindicated.
If the game had depicted that one side was clearly in the right and lorded it over the other faction whether you allied with them or not, that would be problematic storytelling. However, since the leaders of both factions are revealed to be inherently evil at the end, I think it was a refreshing look at the "no way you can come out of this smelling like a rose" ending.