The two QB system was doomed to failure from the beginning. I personally felt CJ should have been the starter from the Purdue game one. KF didn't see it that way, and stuck with Rudock, that to me was the big problem.
Now that this saga has played itself out, it explains some things. I think KF January "depth chart" was solely to let both QB's know it is now CJ's job (and therefor making sure CJ stayed). Rudock knew that much like CJ wasn't going to wrestle away the job from Rudock last year, the same would hold true this year for him. Ferentz knew he was losing one or the other, and decided (wisely if you ask me) that he had to go with CJ.
So I don't have a problem with a QB leaving, that was bound to happen. My problem was this decision was an obvious one since the Purdue game. If CJ had started since then, his feet are wet, and he would be poised to lead this team this year. As it is, we are going to have a green QB going into next year, lets hope CJ doesn't have a bunch of growing pains.