That is the central theme of the mages throughout the games though is that they
are dangerous. It's a choice of do you restrict the rights and liberties of a few to protect the many (specially when you can't be sure if the mage will or not be a problem) and I don't think there is an easy solution. It's right to want freedom and rights for mages. It's also right to want to protect the populace and thus have some limitations on the mages. The question is where do you draw the line which is what basically the Mage vs Templar conflict comes about.
Note: I also add that Act 3 in DA2 is not that well excuted compared to the others and they put the "betrayal" for the mage leader cus they thought they needed two boss fights (though the mage leader is not wholaly innocent wither. i.e he knew about the mage that
was in town and knew something about his research though it's not completely sure if he knew the extent.