I wonder if it's kind of a retrospective angst, with the lyrium issues on the side. Like, according to both his initial blurb and his writer's interview, Cullen spent more than half his life in the Templar Order. And now he realizes that could have just been a wasted effort. All that time, he was serving something that only existed in his mind, but was never actually real. How do you come to terms with that? Can he trust the Inquisition will do the right thing? What is the right thing? Is there a right thing?
On top of that, he's addicted to a substance that will, one day, take his mind. Either because he stops taking it or he continues to, it will happen to him. And it's because of an Order that never really existed.
This is a pretty good analysis,I think that the growing realization that he fought for an idea,that possibly doesn't even exist is also one of the factors that helped him discover his inner strength,disappointment tends to do that to people at times.
It appears that he's also starting to see the greyness of the situation,which is not always pleasant,especially for someone who was continuously brainwashed like Cullen and pretty much every Templar in Thedas.
He's also done waiting for others to act,so he decides to take matters into his own hands and while this sounds like a really "BAMF" thing to do,I believe it's the act of someone who is tired of seeing his ideals constantly crushed by other people's actions.
We still have to wait and see how he's evolves though,but I would expect any sort of retrospective angst,will get worse if the Inquisition doesn't fulfill his expectations.
Which also kind of gives me the impression,that in case the Inquisitor turns out to be an immoral murdering psycho or something,we may even have to confront him.