The problem is everyone always approaches it from the wrong direction, that of mages versus non-mages. Actually the problem throughout Thedas is nobility versus peasantry. No matter what part you are in the nobility ensure the laws are framed to ensure their maintenance of power.
In Tevinter the nobility consists of mages. They come from long lines of mages and their society is structure to maintain their power. Even when mages were not meant to be able to govern, they controlled matters from behind the scenes until eventually they were able to restore their right to govern. I have asked the question, with no conclusive answer, what becomes of the non-mage nobility. The assumption is they fulfil minor roles in government and possibly diplomatic roles outside of Tevinter. Since they are still part of the nobility, there is no incentive to challenge this. The Magisters control the training of all mages, including those that arise among the peasantry and slaves. Either they are elevated in rank or weeded out and killed.
In the rest of Thedas the nobility comprises mostly non-mages. Whilst mages still crop up from time to time in their families, they are the exception rather than the rule and those who do not have mages within their ranks are most likely to support the Circle system. Not only does this stop your rivals among the nobility from having an unfair advantage but also, more importantly, it stops the peasantry from having the sort of power in their ranks that could actually challenge the status quo. On the whole the children of nobles who enter the Circles seem to have a much better time of it than the children of peasants. The former seem to be allowed to keep contact with their families, have certain privileges and even hand picked Templars to watch over them. The latter are cut off totally from their families, have few rights and no one to stand up for them if Templars start to abuse their power.
Whilst it might appear that the Dalish offer an alternative model, it should be remembered that we do not know exactly what happened during the fall of the Dales. We merely have two versions of the same conflict. Because a lot of people are prejudiced against the Chantry, they assume they are the villains of the piece and lying about elven atrocities. However, it could well be that the elf mages, who by this time did seem to be at the head of affairs, may have been indulging in corrupt practices. The very fact that mages were in charge in the Dales probably set alarm bells ringing in the minds of the Chantry, since they had only recently set up the Circles to keep mages controlled and out of government. The Dalish are meant to be the remnants of the nobility of the Dales, with Keepers are the head of affairs who are always mages. This would seem to suggest that elves who were captured and rounded up into alienages were in fact the peasantry and quite possibly abandoned by the nobility when the fight appeared helpless.
So the only way to solve the situation would be to have a much broader distribution of power in government. If at the head of affairs you had a ruling council, with places on it for nobles, merchants, the military, Chantry, mages, artisans, scholars, etc, this would ensure that no one group could grab onto power and keep it by repressing other members of society. Mages would have representation as a group but would also identify with their own sector of society. If you are genuinely living with your family, whatever their rank in society, you are far less likely to take advantage of them or let other people do so. Also they would be far less likely to be fearful of mages as a group. Naturally there will always be bad elements but that is the case whatever you are. If mages are evenly distributed across society they will be policing these matters themselves.