Not to mention the good of the many comes before the good of the few.
Collectivist fallacy. The "many" vs the "one" There is no such thing as the "many". All groups are comprised of individuals. Groups themselves exist only as dynamic and temporary constructs; their composition changes as the individual members come and go. In other words, groups exist not as real entities like a person, but only as temporary, fluctuating social arrangements. A group has no rights, only an individual can have rights.
To be pro mage or pro templar is ignorant. You can support some individuals, or oppose some individuals, but to oppose a group is simply to oppose a social arrangement comprised of individuals, which makes no sense whatsoever. When you lump everyone into a group, you destroy the uniqueness of each person. To say "I am pro-mage" is to say "I support every mage regardless of behavior." And the same with the Templars, and the same with the inverse propositions. To be pro or anti a group is ignorant stereotyping. And this stance allows you to punish or reward those who have earned neither consequence. So let's punish someone for a crime someone else committed, because this person is the same; i.e. black, white, male, mage, templar, muslim, etc.
Compounding this sort of collectivist ignorance of group supporting or opposing, is the fact that there is nowhere any indication as to how many mages, left uncontrolled, as it were, become blood mages, etc. We have no data on this that is reliable, only assumption preached to us by the Chantry and the Templars. Furthermore, these arguments are stupidly and artificially narrowed by failing to think that other possible solutions to the "magic issue" are viable, and perhaps superior to, the Chantry and Templar control and imprisonment of mages.
Finally, this very idea that the many are more valuable than the few created the civil war/mage rebellion in the first place. It creates conflict, and leads to mages rebelling, in smaller and larger numbers. It inevitably leads to power abuse from those in charge, because there are too many individuals incapable of maintaining professionalism and decency when given power over others. In other words, the entire proposition that we should coerce some to save more accomplishes the exact opposite of saving anyone, but rather creates more conflict and war. But then, anyone who even makes a cursory study of history would know that, which makes the whole argument even more absurd.
The wise course is to not create conflicts, but to create shared goals. By making partners, rather than prisoners, out of the mages, you can eliminate conflict creation, and instead create a cooperative atmosphere. This is exactly what Cass and Leliana think about the Chantry and Templars. They both know reform is needed, they both lament what these institutions have become. They were supposed to be helping and supporting, not imprisoning and abusing. But individuals are not reliable, except in the fact that all are corruptible, and most are herd animals. Hence, the inevitable abuse of mages by various templars, the corruption of various chantry members even at high levels of authority, and the mindless following of the abusers and corrupted leaders by many. Viv's desire to rebuild the Circle system is stupid: she can only reset the clock on the next mage rebellion this way.