I actually can really agree with a lot of what MisterJB is saying. It is clear that not all Templar's are evil. That not all Templars are out to kill all the mages and just opress them willy nilly. Most of the mages in the Circle seem to like it well enough. And as has been pointed out they even get a certain modicum of freedom. Is the situation ideal? No, no, no. But I find a hard time being anti chantry or anti templar given the evidence.
As far as the 'no organized resistance' of the mages...that is just not true. Mages, especially who use Blood Magic, are not entirely blameless. And they often travel around in groups and are thus 'quite' organized. The only single Bloog Mage I can remember running into would be Avernus, and we saw the damage he was doing at Soldier's Peak. Which brings us to the current conflict. Because right now, the fraternities have dissolved the Circle of Magi and they aren't fleeing, they are turning and fighting as hard as they can.
Mages who can freeze entire armies or have the power of nuclear bombs in their hands. I can hardly blame the templars for being a bit...worried...at the situation. And panicking. For the first time in centuries mages everywhere is using organized resistance. Thus, the Templars feel forced into using Red Lyrium to protect the people and deal with the new threat. Becoming more powerful to begin with. Is it justified? No, but the Templars are under every bit of preassure as the Mages, given especially that Blood Mages on top of being organized often become Blood Mages specifically to hunt down templars.
The Circle system works on the basis that restricting the freedoms of mages is preferable to having non-mages fall victims to magic.
The ideals of magical freedom work on the principles that, while some non-mages will inevitable fall victim to magic, this is preferable to imposing restrictions on the freedom of mages in the manner than the Circle system does.
They both choose to place the burden of suffering on the opposite side in the name of their own protection. What is the difference beyond that you support one side due to your belief that "freedom is a right"?
At least the Templars have a plan to diminish the number of victims beyond "Let's all be free and hope for the best".
OUt of all the responses I have read this is the only one that I felt compelled to quote. Because you are right, sadly people will not just simply go with 'let people be free' as a compelling argument, especially in this case. Maybe that is why Anders did what he did?
But regardless the mages need a plan, some way of ensuring to the Templars that the people can still be protected. So keep the Templars, keep the Circle, but allow mages to join the Templar Order and also hunt down Maleificar and abominations. Turn the Circles into pure prisons, only for those who are too dangerous and too criminal to be trusted. I think that would be my plan.