The Sox are certainly not blameless in this, but I think when one of your best and highest paid players is resistant to authority it's going to be a big problem, period. It was a problem with Manny, they got through it for years and won 2 rings with him, but in 2008 enough became enough and they traded him.
In 2003, infamously, the Sox put Manny on waivers. At the 2005 trade deadline it was reported that the Sox were offering Manny in trade. I was actually at the game on July 31, 2005 when Manny emerged from the dugout in the bottom of the 8th to a big ovation, having not been traded, and produced a game-winning pinch-hit RBI single.