Think of it this way: The Qun was the only life Bull knew before coming to mainland Thedas. He was force fed since he was little that 'Tal Vashoth are all bad and savages' and a good share of the ones he did fought in Shearon were the bad kind, but at the same time he likely had to put down Tal Vashoth that didn't harm people who just wanted to live there life away from the Qun; which is also one of the reasons why he's scared to become TV himself. If he doesn't turn into the 'savage' kind, then he has to come to the realization that the Tal Vashoth (or at least half of them) were sane and he killed good people.
Bull even said tons of the times that he has to picture those that he did kill as monsters to make it easier to justify his actions. Yes, some of them were that, but what about the rest?
He suffers from PTSD. Most veterans who come back from war are changed in profound ways and aren't the same. They watched innocents and friends die; killed those who harmed them and there's a good chance people get caught in the crossfire at times. This is no different from Bull. AND HE HAD TO DEAL WITH THIS FOR EIGHT YEARS!! Can you imagine how f-up his mind become and then he finally cracked and beats himself up for it.
Also, in regard to the 're-education' conversation: What's interesting about Bull is that while he believes in the Qun, at the same time he doesn't. He was raised to believe that it's the only way to live but once he's given the role to play as a Tal Vashoth merc; he finds that he loves the life of it and it becomes more than just a role. He loves drinking, eating, sex and the friends he made. And that's what fears him.
Remember, his biggest fear is madness; and he's scared he's going to loose himself. And now he's finding he's enjoying his life outside the Qun. He's terrified of that and tries to justify his actions as part of his role that this is all just an act. But a part of him knows this isn't true. His friendship with the Chargers aren't a con, it's real. There his family. These bas are his family and feels as that is wrong. But when the time comes; he has to pick between the Qun or his family. Is he Hissrad or The Iron Bull? Thankfully most of us here chose to save his men, which is also what he wants. He may beat himself up for it in the beginning but by the time Trespasser rolls around; he finally comes to terms with who he is and suppose to looking back; he moves forward.
...I think I just summed up why I ship Iron Bull and Adaar so much...
Also, the mage thing: I think it's the Tevinter mages he has a bit of a problem with and even though if you choose to ally with the rebel Mages he disapproves; he doesn't down right hate them. He was raised to believe that mages are evil; but he doesn't believe that they are. Again with the 'believes in the Qun but doesn't.'
The part after the Fade bit of the game where he asks you to hit him with a stick and you refuse; this conversation happens and there's a party banter with Vivienne about the treatment of Saarebas under the Qun:
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Vivienne: I have heard of the life of the Saarebas, Iron Bull, but I'm curious about your viewpoint.
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Iron Bull: It's sad, mostly. The magic appears late in childhood just like it does for you folks. Some kids go years learning to be a baker, or soldier, or builder and then one day... that's all gone.
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Vivienne: You sound as though you pity them.
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Iron Bull: Well... yes. In theory, they're no different from anyone else. The Tamassrans - and the Ben-Hassrath - protect everyone from their own mistakes. They're people too, just serving the Qun, but too many Qunari are afraid of them.
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Vivienne: Not you, though?
- Iron Bull: No. Everyone who takes that burden and lives a good life with it has my respect
He has no problem with mages. He has one on his team (Dalish)and could end up dating one (either the Inquisitor or Dorian).