So apparently Liman isn't leaving because of production issues or anything of the sort, but rather because Stacey Snider is now head of Fox (as of yesterday) and the two butted heads when Liman was making The Bourne Identity at Universal, which she was the head of at the time.
So, the "mutual agreement" was to let him leave the film so him and Snider wouldn't have to put up with each other. And I'm willing to bet that it was Kinberg who made this deal with Liman, as the two of them are buddies after they worked on Mr. and Mrs. Smith together.