Our prisons are infested with powerful, nationwide gangs, e.g. Aryan Brotherhood and the Mexican Mafia, that make millions (maybe billions) of dollars in drug trafficking. Many of their leaders direct operations from their jail cells.
Now if one of these gangs has a beef with the Colorado DOC, what better way to strike and send a message "don't [...] with us" than by taking down the top man. I'm putting my money on this theory. That this murder was more to send a message to the CO D.O.C. than a personal beef with this Director, who by reports seemed to have been an OK guy.