Actually that's not what happened at all. Barry did change the offense and threw it much more with Troy. It was only after Jerome Brown broke his leg and they had to go to backup option QB Hollieway that they went back to the full time bone and won the national championship. When that happened, Troy wanted out and Barry helped him find a good place to transfer.
For those who haven't seen it, there's a new good long interview with Barry on DC.com. He says all kinds of great things about Troy, even how when pro scouts were talking about this young Jeff George kid was going to be so amazing and Barry told them, I have a sophomore kid better than him.
Edit, here it is: