Some of my personal thoughts when Cullen was saying those stuff to a mage Hawke:
1. Cullen had lived through the worst experience he could get with mages (Uldred's doing). He knows what a tower full of harmless mage but a handful deadly one can do
2. Blood magic is actually able to do mind control. So it's not weird that he gets suspicious
3. He actually said that clearly to a mage. He's honest and earnest in what he believes and how he will act. I'm not fully agree with his point of view but I give him full credit for this.
He does not even hint too you he knows your a mage untill after Act 3. At, best you deflected most of mine and boom's post about making him look like he spouting moderate views points, when he is not.
That's is, in fact, why I would have actually writen the words differently than in the villana game. If they really wanted to show the wisdom he gained; instead of him saying to our Hawke that they and their sisters are less than humans and must be treated differently than you and me.
Have him say, "The Chantry might see mages as wepons to be feared and locked away, but I see them as mearly people that need protection from both the public and themselves, when needed, and this is, why I believe the Templar order was created. Or "The Chantry may see the mages as weapons too be feared and locked away, but I see them as people that aren't like you and me, and this is, why the Templar order was created by the Chantry so we can protect the public from them and also themselves, when needed.