Well in my opinion is that Cullen has just been trying to do what he thinks is right. Ferelden's circle's incident and trauma that followed it just clouds his judgement. His morality was against annulment of the circle but he still chose to follow orders. When talking him before the battle it really seemed like he was really indecisive, like he wasn't sure what was right thing to do and that's why he went against Meredith so late.
Cullen has some views I don't support but I think he's overall good guy and I hope that Meredith case opened his eyes on templars vs mages issue too.
To be honest... this what I like about him. I find it rather unrealistic that heroes always do 100% the right thing without remorse or doubt or consideration for themselves. I think we like writing/watching/reading about heroes like that because it's an unattainable idea.
One of my favorite moments in any fictional medium (which many of you have heard me say about a billion times) is in Pitch Black when our "hero" is almost convinced to leave her flock behind and join the "bad" guy and save herself. She collapses in grief and indecision, momentarily tempted. Sure, she ends up doing the 'right' thing, but in that moment I find her very relateable.
I feel the same thing about Cullen. Sure, the 'right' thing would have been to do something sooner, but I also can completely understand why he was indecisive and why it took so long for him to take a stand. I can't hate him for that, because I'm not sure I could have done much better.