This is pretty meta / me-specific but: [not specifically in response to anything you said don't worry your post just got my gears turning in my head!]
I'm doubtless influenced by the kind of Inquisitor I play, I know - what he intends to do only seems so terrible because we're (well our characters and the world we're invested in) on this side of it.
Anti-tyrant, breaking chains, giving wisdom, martyrdom, saving the People - he talks and is 'talked up' by game lore snippets/companion dialogue etc to be This, and undeniably they're very prominent, strong parts of his character and arc. He definitely will have disliked, resented and likely even tried to combat or at least mitigate the negative aspects of the rule of the Evanuris while Mythal still lived imo, but he didn't seal them away or lead a rebellion against corrupt godkings because he's an avatar of freedom or a savior. What was it that motivated him in overthrowing and sealing them away in the end? The thing that pushed him over the edge to action? They killed his close friend, a friend who was a shining example, to him, of Goodness in the world. That's it. At the deepest level, it was personal rather than a freedom campaign. It became the antityrant / free slaves deal as he made moves against them. He was a man grieving and enraged at the horrific act of his old friend's likely gruesome for-no-good reason murder. She wasn't even removed because she was a despot for some greater good, they took her down because they were jealous, power-hungry, pretenders to her 'throne' [place] in the 'pantheon'. In his eyes they were monsters for this and to him these killers had to be severely punished. I think many people in his position would feel the same way about the people who murdered their friend. So, prideful and in his wrath he acted.
My Inquisitor would absolutely act with such swift and terrible vengeance in fury over the bloody unjust murder of a close friend - say her Keeper, or Cassandra, or Cole. She'd use whatever power she had at her disposal - even if it was world-shaping, like the Mark - to put in place a severe and horrific punishment for the people guilty of such a close-to-home act, likely without care for what impact it might have on others or the world around her.
And then, what he plans to do - only seems messed up cause we're on this side. In his shoes, again my Inquisitor would do absolutely anything, no matter the cost, to protect and save her own people. He says it himself - wouldn't you do the same thing for your own people? The same thing reflected in the duality of the Dread Wolf and Inquisitor fear+hope titles which he also notes. To him it only happened yesterday - imagine you wake up one day and your hometown is destroyed, and there's a different town in it's place, but you could bring back everything you ever loved and knew at the push of a button. It's a sick choice, genocide of one group or the other, but when it's them versus your own? The fact that your town is long dead and forgotten in history is a truth for people in the new town but that isn't the fabric of reality for you. In modern Thedas he wakes up and is completely dissociated, it's plainly stated that it's not real to him, he's underwater talking to people-shaped figures through foggy glass. They're spectres of almost-people, for most of his time there. That's not malicious, it's rooted in the psychological effects of what the **** bewildering world he woke up to. He took up a mantle - freedombringer, iconoclast - and cloaked himself in it til he breathed it, in part for grief, in part for guilt, in part because of instinctive dislike of what the Evanuris were, and to an extent these are layers he keeps between him and the reality of his actions and waking world that he now lives in. Add to this his consuming guilt at what he now thinks is a mistake. And then he notes he takes no pleasure in what he's doing, that he wants the other half to be comfortable in the final days, etc. & how his story - a Not-God who set out to do a thing and was raised to godlike status later for it despite himself - is plainly a foil for the rise of the Herald in Andrastian faith. He's not a monster, he's just the man on the other side of the coin. He's her reflection in a mirror.
Retour en haut
I think they did a good job at portraying that he KNOWS what he's doing is messed up to a mega level but he still finds it worth it. And despite of that, you can still hear some rationalizations because he ISN'T a bad person, he just has the capability and willingness to do some very bad things. All to protect people he gave everything for and is willing to destroy the world for again. You can't say that guy isn't dedicated, that's for sure!
... Though I suppose it could be interpreted as Inquisitor being the 'prisoner' of fate ;P 
