The official version was "artistical differences" or something like this.
The fact is Mandy never made any other statement about his leaving as far I could find. Ed Bernero, the executive producer of the show, on the other hand published this message to fandom via Criminal Minds Fanatic Blog: http://www.fanpop.com/spots/criminal-minds/links/6602762
I'm afraid that's as much as we're going to find out any time soon.

Mandy Patinkin said at first that he was leaving criminal minds due to creative differences, but he later explained that he quit because the show traumatized him. He claimed he could not understand why violent TV was such a curiosity. He believed it to be very disturbing that people go home to watch Criminal Minds to unwind, he wonders how people could consider horrible, mysogynistic, violent activity as entertainment. He claimed that to play such a dark role in such a dark TV show he had to be in a dark place, this dark place he claimed was haunting him, eating away at his heart and soul.


Although he just kind of insulted us, he will be dearly missed.