I have no idea why people don't see why someone might act differently when killing a guard and killing a professional assassin. I also don't know know why people seem to be unable to remember that there is options to criticize the Qun in the DLC.
Yes, you can criticize the Qun, as I have already said. What you can't do is question (or agree with) the role of mages in the Qun to Tallis, and that bothers me. In a game that almost never shuts up about the two groups, you'd figure that you could say something to a member of a group that has the most harsh treatment of mages.
I actually think she wouldn't care about mages or Templars because neither one involves the qun. And I feel like she generally has a not caring attitude about others not believing or following(or whatever) the qun, but this was not really present because of how little content she had. But this does make a lot more sense then that guy above you...
This is all speculation, but I think she would care about mages I think, due to their very strict role in the Qun. Mages are not even allowed to speak, since "demons could ride their very words." Even as something as strict as the Gallows would be insufficient in the eyes of the Qun, since demons could still be lurking behind the mages' words.
Now, gaining control of the mages would be a role in the Qun, just not hers. I could see her spending time trying to convince Hawke that the Qun is just "going to help those poor people." How she would justify that to a mage Hawke, I don't know. That's another theory I have as to why they didn't give the player the option to question Tallis; she wouldn't have had good answers for Hawke's questions.