The 'mages will just kill all those commoners' crowd forgets we already have historical precedent for what happens when mundanes decide they don't like mages living among them.
The mages get slaughtered to the point that they run to the Chantry for protection. In fact, life outside the Chantry is so horrific for them that they are willing to accept life as little more than candle lighters rather than face the continued persecution.
This is the same group who demanded the creation of the Circles to give them a place where they could live, practice magic, and not get burned at the stake by angry mobs. A practice that can still happen in modern Thedas, apparently, if the Templars don't arrive in time.
Yes, a fully trained battle mage is a force of nature. But most mages don't have the level of skill or talent required to be a battle mage, and no mage starts out as one.