From what I gathered Cullen knows what's right and that's protecting people I think that he doesn't know the best way to go around it. He was betrayed and tortured by Mages and that drove him to a more Templarist approach and now that he's been betrayed on that front because he believed in Meredith in a way before she went crazy. He may become a lost soul, not searching for a purpose but searching for a way to fulfil the purpose. Or a more poetic way of putting he sees the light at the end of the tunnel but he does not see the path.
I agree that he wants to do the right thing and may not always know the best way. I tend to headcanon him in Act 3 as constantly tortured about what to do about Meredith since he told himself he "would never again question the Order." And yet, he obviously is. Poor guy.
In this case, though, I really believe the right thing to do about Thrask is set the record straight. Meredith is on a witch hunt. No matter what you say or do in this quest, she's not even after all the 'bad' mages. She's after Orsino, full stop. Letting her think that this was just a mage thing would have let the situation blow up even more. Probably triggering the Annulment earlier.
I also tend to imagine that finding out your own brethren were rebelling against the Order would be a huge kick in the gut for Cullen. But I don't imagine him hiding from that truth. Rather, I see a big ole House Cleaning in store for the Gallows, as far as he's concerned.