Because Fiorentina didn't like Gattuso agent messing with their transfer policy (Mendes)
Mendes may very well be cumbersome, but honestly, Gattuso doens't strike me as the type that's in it to shake a club down with his agent first, and do his job as a coach distant second.
Rumour has it that it's all about severe personal frictions that heated up the confrontation on trasfer strategy, rather than the mere decision of going all-in on Team Mendes or not.
Fiorentina is also a bit of a hydra at the moment, they're restructuring the club's pool of directors - Burdisso is coming up from Boca to partner Pradè, Antognoni is expected to not renew his contract after being offered a reduced role, then there's Joe Barone that's supposed to be Commisso's right hand man but it's not clear how much personal latitude he puts in the role...
Commisso is ambitious and seems a good thinker of an owner, but he's still struggling to figure out how to turn Fiorentina into a well-run club.
Reportedly the board already rubbed Gattuso the wrong way just before he signed, prompting him to renounce and then u-turn only because of strong personal backing by Commisso. It seems things never really worked right from there.
None of the parts involved is looking much good going out of it this way, granted.