With the exception of annulments most of those acts are not legitimized. At least not formally. I doubt the Aequitarians would be as dominant as they are if those atrocities were something every mage felt was a given as being part of a Circle. These aren't things the Templars could do willy nilly with everyone within the establishment being knowledgeable and permissive of them. We've no reason to think that's actually the case outside of some isolated cases. All this proves is that the Circle system is in need of reform so that these people don't undermine the good that could come from their existence (I think it'd work best as a mandatory educational institution that prepares mages for safely existing within society).
Frankly, I wouldn't be surprised if the current climate allows for mages to be abused more out in the open than in a Circle; what with so many contributing to the chaos. Even with the Red Templars, I feel like the mages will get the short end of the stick when it comes down to placing blame.the
Aha. The blatant abuse and mass-killings aren't always formally legitimized. I guess it's not such a bad system after all.
Ever heard of Stockholm Syndrome? If you had been at the utter and complete mercy of brawny, heavily armed, self-righteous drug addicts who hated you for being alive from early childhood, would you seriously go around talking about escaping or rebelling, much less join an open society for fellow prisoners who felt the same way? Of course the majority of circle mages are self-professed Aequitarians, they're scared out of their minds. I agree that a reformed Circle system would be a step up, but such a reform would never be possible without a rebellion in the first place.
Your argument being that since they can get hurt and get a bad rep defending themselves, they should obviously just submit to slavery and genocide? I don't know which mages you're talking about, but the ones I know can throw lightning and heal each others' wounds en masse. I'm sure they'd politely appreciate your concern. 
I guess some people would rather have some dumb "yes sir/ma'am" mage than a mage with ambition and intelligence. People like Thomas wants a lackey to push around. When he says, "jump" the mage says, "a normal jump or with a spell?". Vivienne would never put herself into a position to become a lap dog.
If you want a lapdog then perhaps the other mages will suffice. I'm also willing to bet Morrigan wasn't your cup of tea either, huh?
I want trustworthy, reliable agents and advisors when I'm trying to save the world, thank you very much. Not only is your comment incredibly presumptuous and rude, not to mention poorly articulated, but it also completely misses the point. I liked Morrigan just fine, mostly because she was beautifully written, but one Morrigan is enough and the stakes are supposed to be higher this time. If your inquisitor doesn't take the mission seriously and surrounds him/herself with nutcases and extra-special snowflakes with no thought to actual effeciency then that's their headache, and yours too, I suppose.
It does make sense. The mages are not fine they are at war not only from templars but from Red Templars too. Also demons are a much larger threat to mages than to anyone else. Also joining the Inquisition will step on everyone's toes because they are a rogue group who are basically there to do everyone else's job for them. Why is her former influence negated? She's not the only mage who supports the circle system and who doesn't want war. We have a Tervinter magister and an elf fade expert who I am pretty sure is an apostate.We don't know what their views are or how reasonable/reliable they will be. Who said Viv is unreasonable though? Who said Viv was unreliable?
Everybody is at war, and unlike everyone else the mages have magic, which is, as I'm sure you'll agree, pretty handy for defending yourself. Why are demons a larger threat to mages than anyone else? With them having direct access to the physical world now, the likelihood of demon possession should decrease dramatically. If anything, mages are better equipped to deal with them than the rest. Joining the neutral and completely unaffiliated Inquisition allows her to influence the order in favor of her prospective benefactors and leave whenever she wants, and should the Inquisition actually succeed in its goal then she would end up with even more authority than she had before, and even if it doesn't, she'll be able to ride events out and then join the winning factions denying that she ever sided against them, no matter who wins. Her former influence is negated because her country is undergoing two entirely seperate civil wars. She might be able to throw a small party and keep up on current events, but no way her power, or anyone else's for that matter, extends much farther than that with Orlais in its current state. Vi is unreliable because she's an ambitious connvier who apparently supports a disastrously cruel, corrupt and faulty system for her own benefit. That's it.
This. Also saving Thedas would require more than magic and swordplay.
There's plenty of magic to go around. She won't personally make that much of a difference, and if she's more trouble than she's worth anyway...