Honestly, the short story with Anders feels as though it's divorced from the narrative of Dragon Age II. Queen Anora and King Alistair are sympathetic to the plight of the mages. If the Warden-Commander is pro-mage, than it makes even less sense that the order would acquiesce to allow a templar spy into the organization. If the Warden-Commander is a mage, I'd think having a mage having political power as Arl, as well as commanding an army and governing a city, would be more of an issue for the templars (and even the Chantry) than a single mage serving as a Warden.
Excactly, Anders is still considered to be a warden by to many wardens. And the first warden would never be careless enough to fall for a chantry spy, while the Grey Warden order is trying to take over Anderfels.
His behavior is nothing alarming in templars organisation because almost every templar is fanatic and i want point that despite that many sociopaths and psychopaths despite being hostile when they are not on sight aren't recognized as such even by family or friends.So arlik didn't had to run around screaming what he was doing...
So you are telling me the chantry is allowing insane and dangerous people to become members of the templar order, thus safeguarding humanity from evil mages and certain doom, while they are spreading the chant of light in order to safe humanities souls. So our fate is decided by fanatics, religious zealots and psycopaths. Well, I guess that´s something.