@Riverdaleswhiteflash; I don't know what faction within the Libertarian party is the largest - those that want more autonomy or those that want to altogether split from the Chantry - but either way really its never enough to end reform at plucking out the bad seeds from the Templar Order. I don't think the more radical Libertarians - even if in the beginning they wouldn't kill to meet their goals - can ever be persuaded out of their position because their position is about control of the system.
The burden of justification for status quo falls on the Chantry in this dispute and the Chantry's arguments just aren't very good at this point. The reform of the Cassandra and Vivienne endings may not last, IMO it won't, because the same power structure is in place. The distribution of power within circles and even within the system hierarchy might change somewhat - so mages with more power in their circle and mages with power in the Chantry itself - but in the end you still have circles under the Chantry and everything that means with it.
Even if there are Libertarians that say initially they wouldn't kill to free the Circle, I don't think they can ever be expected to stick to that, and if they see a chance at revolution, of course some will take it. They may try evolutionary means first - redistributing power in the circles and in the system - but if that doesn't work or they recognize they shouldn't discount revolution because under the right circumstances it could succeed, they're never going to take a conservative position on the Circle.
And part of the status quo or even reform, I see, is the manufacture of consent - to get mages to not listen to those that say the circle should be altogether free by removing or marginalizing those groups or individuals in some way and then limiting the fallout of those coercive actions. Its hard to defend a system that has to go to such extremes to maintain itself.
The ones who want more autonomy should be free to make suggestions and have them seriously considered. I think we agree there. The more radicals... well, the Templars can try to explain why it is they do what they do. The actual Libertarians might or might not listen. And if they act on what they feel in a way that puts people in danger, they can be dealt with. The more quietly the better.
Okay, we've mentioned that mages without training are more likely to go abomination, and that if a mage does go abomination in the Circle at least the people around are for the most part able to defend themselves. We've mentioned that while it's impossible to get all the mages, the Circle can probably get enough to make a difference. We've mentioned that free mages have caused disasters like the Lady of the Forest and Hakkon Wintersbreath, even though I think it's the weaker argument than the abomination thing. We've mentioned that some mundanes hate and fear mages, and that not all of that is the Chantry's fault and therefore not all of it can be stopped by changing the Chantry's position. Did we need more than that?
As for Cassandra and Vivienne's reforms not staying... why wouldn't they, at least for a while? The mage rebellion was a serious threat that happened because the Chantry cracked down hard on all the mages for something only one of them did. Keeping their goodwill, and limiting how desperate they feel, is a logical method of avoiding another such problem and if it works why wouldn't it continue?
Eventually there will probably be more mage revolts. The key is to keep them small so as to prevent crap like the kind that nearly necessitated the Annulment of the Ferelden Circle. Part of that is what you refer to as "manufacturing consent," and which I call "reasoning with the mages." And while I included assassination in the list of ways that can be done, I can't stress enough that I'm only advocating that for people who the Templars could prove were willing to kill if they didn't die first, if the Templars were caught. (Note that I'm also advocating that the Templars not do this if they could get caught, since that might necessitate more dead mages; the reason I'm advocating for assassinating dangerous mages one at a time is because I want fewer mages to die than Uldred and Adrian caused with their half-baked schemes.) I'm not arguing for doing any of this to limit the more benevolent Libertarians influence, since that isn't worth killing over. And of course the other side of the coin is that I'd be willing to consider forced Joinings (at best) for Templars like Alrik who should never have been given authority over the mages. I'm willing to concede it's not only the mages the Templars might need to be harsh with; the fact that they've forgotten their fellow Templars might need forceful handling is part of why the Mage Rebellion happened.