As far as I know (which isn't very far in this regard) one of the main reasons was Kirkman didn't like the changes he was making. The CDC plotline (Kirkman doesnt want to explore the technical side of the "virus", nor the origin), as well as some of the zombies displaying more advanced behavior (such as smashing the window with a rock). I've heard Darabont can be a nightmare to work with, but he had great rapport with the bulk of the main cast in season 1. Enough that some (Laurie Holden and Jeffery DeMunn in particular) wanted out once he left. Seems the only bigger loss would have been Kirkman himself.