Personally, I think he was stunned by what had just happened. His mind was blown. It was another confirmation that not everything in his world was black & white. They had just fought side by side in a bloody battle, and he just...let them go because it felt right. I always imagine him second guessing himself as soon as they are out of reach, though. Not in a "I must give chase" kind of way, but more like "did I do the right thing" kind of way.
I always imagined that Cullen found it hard to reconcile his preconcieved notion that "Mages = Bad" when Mage Hawke continuously acts as a force for good in Kirkwall, especially if the Hero of Ferelden was a Mage Warden as well.
Cullen always strikes me as a guy who desperately wants to believe that the Templars are right about Mages being dangerous because it would make his job easier, yet finds himself constantly doubting it, especially when he sees Mages outside of the Circle acting genuinely heroic of their own volition.
And even if a Mage Hawke keeps Anders alive, it's clear they aren't fighting for his revolution and are furious at him for what he did. Cullen definitely had his eyes opened at the end of DA2 that the world has far more shades of grey to it than he would like to admit.