Torre's former bench coach Don Zimmer, now a senior advisor with the Rays, said he was also cheering hard for the Yankees. Girardi broke in as a rookie catcher with Zimmer's Cubs in 1989 and went along with him to Colorado in '93 before continuing with the Yankees in '96.
"I was pulling so hard," Zimmer said. "I spent the first 10 years he was in the big leagues, we were together. Joe's quite a man and a very good friend of mine. I was happy for him and I was happy for the Yankees."
Zimmer noticed the scrutiny on Girardi was intense during the Fall Classic, and he said that he was pleased the manager was vindicated in the end.
"He took a lot of heat from the media during the Series," Zimmer said. "I remember all that. [The media was] second-guessing every move he made. If they'd have lost, I'm sure he'd have heard more. Now that he won, he's on top of the world. That's the way baseball works. I was so tickled he was right."
OK so he was rooting for Joe Girardi specifically, but to me that still counts as rooting for the Yankees.
It's also mentioned in the article that Joe Torre was somewhat relieved he wasn't forced to manage against his former team.