I know the Templars didn't actually do it, but it's not from lack of ability. They simply didn't have the right numbers and Gregor was waiting for reinforcements when the Warden showed up in. Since the Warden couldn't wait, he pretty much said: "Things can't get any worse. If you'd like to try to save/slaughter the mages before our reinforcements get here? Go ahead. If you succeed, that's one less annulment that we have to perform. If you fail and/or get killed? Not our problem."
That is your own interpretation just as mine was that of the Templers being too weak, if they had to wait for reinforcements (that were not coming by the way, you know blight and all..) then they could not have annulled the circle by themselves had the Warden not intervened they simply lacked the numbers, therefore my deduction is: no warden = Templers being abomination chew toys.
And yet the Templars are able to wipe out the mages. So much for being "inferior." 
And I'm sure every Circle that has ever been on the receiving end of a Right of Annulment would agree with you. You know, if they were still alive.
Yes it’s not the first Annulment in history, and if the Templers weren’t systemically making sure that mages were untrained for combat then many Annulments would end in Templers demise, though i applaud them for thinking ahead and denying their prisoners the chance to master marital pursuits in the end mages have a wider variety of uses in combat and therefore are a more useful resource, at least from my tactical view point.
Of course, actual social norms are often far from the social pretensions that groups like to adopt- or what the player, often a well-educated and relatively affluent product of western liberalism, expects. (And, let's face it, western liberalism is the primary target demographic for the luxury products of this Canadian company.)
What is claimed, and what is actually a norm, are often two different things. Corruption is a frequent case: few societies boast about being corrupt, but corruption can be a dominant and even expected trend. Corruption is often a means to taking care of friends, of family, of providing resources to 'your' group as a responsible and helpful member of the group. And that's not even considering the criminal underworld, a norm which is always hidden under the surface.
Mind you, my ideal character arc that I want to see isn't a character who changes towards the player's position- it would be a character who moves away from it on the basis of what the player isn't. A yin-yang relationship of sorts. If the player is a moralizing do-gooder who stands for the innocent, then the character will be a more cynical reaction who comes to believe that someone needs to stand for the not-innocent as well (since, say, most people are assholes and it's not moral to just save the nice and sympathetic ones). Whereas if the player takes a more 'evil' route, the companion would become more of a knight in sour armor, being the good person because someone has to.
And that's not even considering the potential of a corruption arc, in which the player's influence, possibly for the best of intentions, bring down a good person.
Indeed players tend to project their own modern world view into the games they play, even when its grossly inappropriate, I personally believe that a player should inspect the fictional universe of said game then their characters background and last but not lest the society in which said character grew, then and only then should you form your character’s morality, you can still have a "good" morality it just needs to make sense in said setting.
And partnership based on a yin yang aspect would be quite fascinating to explore, and having a reactive companion instead of a passive one would also increase any replay value the game or said companion provides, i approve.
@OP:
As a rule, I really dislike redemption stories. The main reason is that all too often, when more "grey" characters are involved, I don't agree about there being a need for redemption in the first place. If it is about having been pragmatic, I often perceive the Atoner mentality as a needless guilt trip about things you should acknowledge as having been necessary at the time, even if you wouldn't do the same again in the present.
The other reason is that within a redemption story arc, an ideology I like is all too often denigrated along with and by the methods it has used to gain power, even if there is no necessary association between those methods and the ideology itself.
I am fan of grey characters who stay grey. Neither do I want them to cross the moral event horizon and become "villains", nor do I ever want them to conform to a more conventional form of morality. Whether I agree with them or not in any single case, I highly value if someone has their own personal ethics which is independent from the mainstream, as long as it makes sense to me and I can agree at least with the principle it's built on. Most redemption stories are about making a turn away from that to a more mainstream morality.
If it is about "evil" characters turning about, then all too often I think that it's impossible to make up for the past because the damage is done and irreversible, and redemption in that sense is a delusion. All you can do is do things differently in the future, and that should be enough. Drowning in guilt about not being able to do more doesn't make any sense.
And lastly, guilt is all too often used as an indoctrination device. To use a RL example, take certain Christian churches' attitude towards sex. A typical example of inducing guilt about things people can't change for the simple fact it's built into their genes, because they're human beings. I perceive this kind of thing as a tool to gain power over the minds of people, and it is among the most detestable things people can do to each other. The need for redemption may or may not be justified in any single case, but guilt as a motivator to do things remains thoroughly suspect in my eyes.
What you describe reminds me of a nietzsche's superman (or Übermensch), a character that declares that he or his objectives should not be hindered by considerations about good and evil. Such "meaningless, fallacious false dichotomies" are for simple-minded beings, not for him. He often terms them antiquated or childish propaganda, and may go on to question What Is Evil?
Though writing such a character in a companion role and giving them biowarein (is that a word?) depth is no easy feat, it is much easier to cast them in a antagonistic role, i still hope to see such a character as a companion one day....a man can dream cant he?