I think the Qunari just needs to make membership within their society optional. I know it's not possible since the core of their religion is that everyone not like them is a "thing" that need to be enlightened by joining them, and they'll force you to join whether you want to or not, even if they have to brainwash you with poisonous gas... but it's fun to speculate.
I think the Qunari have a lot going for them. They have a society where there's no joblessness, homelessness, or poverty since everyone has a place and they find you a place if they don't have one. If you're physically or mentally disabled, they'll provide assisted living; they treat all races equally; they don't consider some jobs or people "more important" than others (unlike Thedas' aristocracy, where they believe only some people matter); everyone has a basic living wage and food on the table; and if you're really unhappy where you are, they'll usually let you switch jobs within limits. To much of Thedas' impoverished and enslaved (and elven) population, the Qunari seem like a better deal than blatant oppression (like slavery) or inescapable poverty.
Honestly, if I lived in Thedas without magic and wasn't an elf, I'd actively seek the Qunari out, because a society where I'm pretty much guaranteed food, shelter, and a job suited to me in a world where most of the population does backbreaking labor for scraps or starves doesn't sound fun.
My problem is that they try to force everyone to join their system whether they will it or not, and try to force them to conform if they're not happy within it. That's not okay. Their horrendous treatment of mages and their expectation that everyone has to abandon all their previous religious and cultural views and practices (like elves), also isn't okay. If the Qunari just stopped trying to forcibly convert their neighbors, didn't attack anyone who tried to leave, allowed converts to keep some of their old cultural views (like elves), and weren't so heinous to their mages, they'd be pleasant neighbors to everyone like they are to the Rivaini, and probably be seen as a better deal to overworked serfs, slaves, and other oppressed classes in medieval monarchies. As they are, though? By constantly attacking and trying to forcefully convert everyone, their neighbors fear and hate them, and their citizens resent their constant oppression.