I was out of the country for his first few weeks on the roster. What events in particular are you referring to?
From what I've read, Joe irritated some in the organization more than usual this year because he said things in pubic that were either not supposed to be mentioned or that didn't represent the organization's viewpoint in the correct light.
As an example, again from what I've read, the Bernie Williams incident during Spring Training did not present the organization in its best light, but that was supposedly Torre's doing. When Torre finally invited Bernie to ST, it looked like Torre was the one supporting Bernie's return, when in actuality it had been the organization.
With Chamberlain, the 'Joba Rules' were never meant for public consumption.
Also, I guess Chamberlain was used in Game 3 of the ALCS. Some people felt that was unnecessary with an 8-3 lead. Chamberlain came up sore the next day.
It seems to me like there were series of issues that after 12 years reach a point where it's best for both parties to move on.