When it comes to Templars and Mages, both side have compelling arguments, and it all comes down to what one's find morally acceptable.
However, it does seem a little illogical to be, rightfully so, appalled by Anders's murder of hundreds of innocent people, while at the same time cheering for the murder of other innocent people (for the most part at least), just because they happen to share a genitic trait with the culprit.
I don't think the Circle, as it is now, works anymore, and the fact that it has "worked" (at least for the mundanes) for a long time does not mean that it should be exempt of reforms if reforms are needed. I never even really understood why mages needed to sever completely all ties with family and friends. A trauma such as being torn from your family just increases the odds of creating unstable people, and folks that love their kids will do anything to hide them. Even if you don't aknowledge the moral issues inherent to this kind of system, it just seems utterly inefficient.
Obviously the mages need training and supervising, but at the same time, it seems quite hypocritical to treat them all like "cursed" dangerous criminals, and then ask them to go lay down their life every time you need them to go to war, fight the Blights, etc. Or even to allow the ruling class to use mages to attend to their needs, while denying citizens all the benefits they could get from having hospitals runned by healers, for examples. Every time magic is discussed, it seems the focus is sorely on the bad, while there is so much potential for good.