The Circle, hmm... I remember a certain quote(I looked it up before quoting it incorrectly)
“The Circle is a prison. You have choices... between joining and suffering various deaths of body or spirit.” ―Mouse
Fear is going to be the back breaker of freedom. No matter how many progressive or quasi-progressive reforms there are and will be, fear lurks in the crevices of the memory, like a tumour. Detected, recognized for what it is and can cause, but categorized as "benign" until it is no longer benign. How many kids go to "mandatory" schools with the freedom to go home and still skip class? How many go to secluded schools and still skip classes?
The moment a person develops an affinity to magic... the tumour rears it's head from being benign. It's there, like a hair-trigger. People or beings who developed an affinity to magic had never asked for it, but it happens. The circle(as far as I can see) was to help and encourage them be or become a part of the society that feared them. The chantry and it's templars should have been like a guardian or parent to the circle. Encouraging and helping, instead they nurtured and cultivated the fear, which metamorphosed into outright hate and prejudice(as if there isn't enough of prejudice already). The risk of an uncontrolled Mage or a Mage not in control are there, and real. A Mage overcoming the harrowing and considered "safe" to live amongst society going against his/her establishment are just as real, and pose the same risk.
Many fail to realise, Freedom means different things to different people. My opinion, Freedom is not a state in which one is placed due to rules and regulations or reform(as it may be). No, it is a state of mind. There is a saying, "Freedom is what you make of it". In Vendetta there was a statement I liked a lot, "An idea cannot be killed...", but I think it can be reformed. There are ways to sterilize the water in a bottle without emptying the bottle first. Either you sterilize the water(magic) before it is poured in, or you proceed to sterilize the water already in the bottle. Some may argue that sterilizing the bottle too would make sense. That may sound feasible but in the case of magic, not sound. Some develop an affinity at birth, others later.
I theorize that magic in itself is not corrupt. However, you can corrupt magic by way of education(Society, Chantry, Circle, Family, Personal experience). The thought should be, how do you teach Freedom, and not how it would work. This is just my theory(game lore theory) on this subject though.