I don't have a problem with MotA. There are quests in the main game, that bugged me more. Like when I suppose to help Isabella, despite her being the reason for the bloodbath at the end of Act 2. I have much more respect for the Arishok (even as a mage), than for Isabella. At least, the Arishok does not claim to be my friend. So I gave Isabella over to the qunari on my first playthrough and was disappointed, that she managed to escape again. Don't get me wrong - most of my Hawkes are rogues too and they wont loose sleep for stealing. But letting a bloodbath happen, when I could stop it by handing over the book, is just all sorts of wrong. That's why I never understood Isabellas popularity (okay, I'm a straight woman, so her two main arguments are totally lost to me
) and that's why I have no problem with Tallis at all after Isabella.
But I can understand the argument of the threadstarter, I hate it too, when my character does something, she would never do.
About Mage Hawke not making sense: When I play as mage, I use a mod, that conceals staffs (not just Hawkes, but Anders and Merrills too). So when I enter the gallows, I'm just a nice young woman, taking a stroll - nothing suspicious. And I guess, the two times, a templar is nearby, when you fight, is, when you help Cullen against the abomination and when you safe Emerics hide. If either of them would spill the beans, that would be very ungrateful. And Cullen seems to be a bit mental unstable, but he has honour and Emeric does not seem to care about anything else than his investigation - he seems practical enough, to accept the help of a rogue mage without asking too many questions.
In Act 3 Meredith is telling you that she knows, that you are a mage. If I remember correctly that is, how she gets you to do her quests, even if you refuse (and if I remember correctly, she will threaten you with Bethany, Anders or Merrill, if you refuse as a nonMage Hawke). She says, that she wont be so lenient any more, if you don't do the quest - so I guess, the Templars in Kirkwall are a bit thick (most of them certainly are, with the exception of Thrask maybe), but they find out eventually.