For what it is worth here is my perspective on this whole thing. First I have a senior in high school who has been accepted and plans to enroll at UM in the fall. However since being accepted and making the decision to attend UM these multiple allegations have surfaced, and frankly so have second thoughts about if UM is the best place for my child to go. While I would not have advocated for firing either Pflugrad or O'Day based on what little I know of the issues, the changes being made at UM have restored my faith in the University, and in Dr. Engstrom to get this mess cleaned up. Remember that in addition to Pflugrad and O'Day, Charles Couture, Dean of Students, is "retiring" and Mehrdad Kia, Associate Provost of International Studies has "stepped down". Just as with the O'Day and Pflugrad firing, UM denied these changes had anything to do with the rape allegations or how they were handled, just that it was about time for change.
As far as why Pflugrad and O'Day were fired, I don't have any inside information or real knowledge, but a picture is becoming clear to me, and to speculate I think you need to look no further than their reaction to getting fired to see why. Pflugrad's reaction was shock, anger and disbelief. He was in fact clueless that he could be fired for what was happening. His cluelessness was made obvious with his public comments about Jordan Johnson's character, pouring gasoline on a fire that was just getting put out by Jordan's lawyer, and resulting in a letter from the girl's attorney to the University and the Press. regardless of Jordan's innocence or guilt, Pflugrad should ave known better than to pour gasoline on a smoldering fire, especially when seemingly the whole forest is on fire. Pflugrad didn't "get it" then, and based on his post-firing comments he still doesn't get it. And if he doesn't get it, he can't be a catalyst for the change that needs to happen to stop these issues from occurring.
O'day's reaction has been that of the loyal professional, refusing to say anything negative about either the University or Dr. Engstrom or the process - LOYAL TO A FAULT - the same loyalty he showed to Pflugrad, and that fault, I believe is why he no longer is athletic director. In hind-sight it appears clear that Dr. Engstrom had doubts, probably since these issues first arose, about Pflugrad's ability to manage the football program and make the changes needed. Clearly O'Day, being loyal, has defended Pflugrad to the end, until it became clear to Dr. Engstrom that his instinct on Pflugrad's ability to make changes were correct, and further that Jim O'day, being loyal to his coach, would never make the change either. He was left with 2 choices - fire both of them, or let the problems continue. He chose to make changes to solve the problem.
Note that I have not made any judgement on guilt or innocence of Jordan Johnson, or any of the other players. Their guilt or innocence doesn't matter in this case. It was sensitivity to the issue, and dedication to change the culture that mattered, and in the end Pflugrad and O'Day's inability to make changing the culture the highest priority I believe that is why they lost their jobs.