They attacked a major city killing a crap load of innocent people and started to forcibly make people convert the Qun, if they did nor ojin they killed them.
Their plan in Tresspasser was to kill all heads of state then convert the south. How is that "atrocious" to you? That's what they have been doing since DAO, that's their goal.
And no, it's only a equal opportunity to non-mages.
They attacked a City after years of provocations, veiled threats and a long wait trying to get back the tome of Koslun. That's actually a lot of patience here, a lot more than most humans have shown us so far.
Their plan in Trespasser, while brutal, is not so different from what the South would do if it could. Plus, it would lead to the end of wars between countries which have been at each other throats every few decades. And killing some few peoples to ensure that the resistance would be weakened is a good strategy. Isn't it better than what the humans did at the end of the New Exalted Marches, when they killed thousands of converts instead of trying to build a more inclusive society, and yet try to pretend to be more pure and correct in their ways than the Qunari.
As for the mages in the Qun... so what ? Do you think that the Saarebas aren't at least proud in doing their duty for the Qun, despite how they are treated ? Do people like Vivienne or Solas truly deserve to rule over the others simply because they can unleash fireballs at their whim ? The life of a Saarebas is atrocious, but isn't better for the whole society than to suppress mages in towers and then have to kill the whole population apt to use magic in a country when something goes wrong ?
The Qun is far from perfect, but out of every society shown so far in Thedas, it seems far better in all the possible ways.