First, maybe I am missing something here, but on what are you basing your assertion that an OC cannot do his job along with this Penn State deal unless you sit in the meeting rooms and see what everyon'e role is? I am aware that the Penn State role takes time, but an OC delegates just like any other good supervisor (BB actually said in "A Football Life" that he explained a detailed plan to Parcells, who said "don't like it" and little more - How much time did that take?). Absent that critical information, you are attempting to line up what many would characterize as bad execution on the field with a flawed game plan, or that the management if flawed is a product of strained time resources. The Pats coaching staff is not three people, and I have never seen any details on their day-to-day responsibilities that would support your conclusion. People who delegate have more free time because they supervise the overall product rather than getting mired in minutia (which they tend to be capable of reviewing quickly). If you have some insider knowledge on those responsibilities on which you appear to make your logical leap, do tell.
Second, Brady does not simply run a play and throw to a particular receiver. If Slater was a diversion, and Brady hit the open receiver, then the play would be brilliant as the diversion would be effective. Brady walked on the field and threw the ball to a lesser receiver with admitted rookie-like tunnel-vision. BOB did not tell him to do so. That reflects Brady's bad decision-making on the play. Throwing to Edelman? Brady's decision-making. Suddenly Brady, after all his success, is a mindless drone on the field? That isn't a reasonable proposition, and is inconsistent with past accolades he has received when he suceeds. As he admitted, he had a bad game and rarely does see games like that. Is the game plan bad because it didn't work because the personnel groupings were unworkable or because options with those groupings were improperly utilized by Brady? Brady always says his favorite target is the open man. Was that the case in the examples you cited?
Third, running success appeared to come when Ngata was not on the field. I would like to see the stats on runs with him on defense and runs without him on defense. The Pats were not running amok on the Ravens D. They had 96 total yards and a 3.1 average, which is not lights out by any stretch of the imagination. Green-Ellis had a few long runs, but that was offset by bad runs to a 4.5 YPC in 15 carries (I submit the 2nd ranked run defense of the Ravens would have further lowered that average if the Pats went run heavy on play calls with predictable running plays). The overall plan was fairly balanced, at 31 runs to 36 passes. So would your preference be run more, run Green-Ellis more, tell Brady to check to runs or not check from runs, or what specifically? What would a competent, well prepared, non-time-stressed OC have done in your opinion?
I submit the offense played poorly and did not execute, and Brady immediately acknowledged that. We credit Brady regularly as a field general, and the point of your post seems to imply he is simply running a designed play that cannot and does not vary with reads. Hindsight is 20/20, and organizing a lynch mob against BOB because of his follow-on role ignores the basic reality that Belichick is well aware of what his OCs do, is well aware of his coaching staff's capabilities, and is the paradigm of success in running teams to championships. If anything you have ever seen of Belichick leads to the conclusion that he would allow a coordinator to accept a different job and run his team into the ground during the most significant games of the year to the team, then please point to those facts. BB cuts players with storied careers and runs coordinator roles himself as cold business decisions. If there was some issue he could not personally handle with the current situation, then he would hand the job to McDaniels and let BOB go. His decision not to do so implies all loose ends are addressed, unless you assume Belichick himself is acting out of his love for BOB and has lost his way as a head coach.