This is the only explanation I've seen for Nix still being in place that makes sense. We have Brandon taking over who has watched Nix fail miserably for three years, and who is pushing an analytic system that Nix knows little about. Together with the information we got from their choice of Head Coach, a scenario in which Brandon has allowed Nix to remain an all-powerful GM seems farfetched.
So why is Nix allowed to continue to collect a check and pretend to be General Manager? Your scapegoat explanation makes a lot of sense.
I'll also throw out there (as has been pointed out by GG) that we had our best draft in a number of years in 2009, getting Wood, Byrd and Levitre under Brandon as de facto GM. No doubt Brandon is aware of this fact. It's possible that Nix as figurehead GM allows Brandon to again take direct control of the football operation.