There are two possible scenarios that spring to my mind:
1) Jean Todt leaves Ferarri to provide "separation" before taking on the role of FIA president, promised to him in exchange for shafting the other teams that were forming the break-away F1 and signing the Concorde agreement.
2) Jean Todt leaves Ferarri because he's incompatible with the de-sleaze cleaning operation that Di Montezemolo is performing at Ferrari, equalizing Ferarri's position in Formula 1 with that of other teams.
I'm hoping it's the latter. So far Di Montemezolo has done a lot to stop my utter despising of Ferarri for its history of backroom F1 dealings. Jean Todt was very much a driving force behind the whole sleaze thing that's driven me to the point of abandoning F1 in disgust a dozen times or more in the past.