Scott needs to lead, and Hank has to be the one to tell him when he's going too far. Problem is, Scott wasn't confiding in Hank a damn thing. It's difficult to be the voice of reason when your leader won't turn to you for advice. While Scott was running X-Force and Emma was meeting with Osborn, Hank was left behind. He had to figure out their secret arrangements for himself, bring them to one another's attention, and then show his disapproval. The lack of trust that anybody showed in him is part of the reason he walked away.
Also, I'll be the first to admit that he got kinda pissy about being tortured by Dark Beast. When Hank got rescued, he kept turning to people like Scott and Bobby for comfort, but nobody had the time, so he ran away to the arms of his green-haired ho.