It comes down to this: The eventual apology was a direct result the emergence of more and more confirmation of Brandon's version of events, including incriminating pictures and more video. They had no choice but to apologize at that point. Had those pictures not come out, I'm pretty certain they would have stayed with the "protecting the player" story.
After it happened, anyone with any common sense would have said, "Yeah, I did it and I'm sorry", and the whole thing would have been over in less than 12 hours. What made it drag on and get bigger was the reflexive cover up that was going on: Ignore, minimize, and finally, just flat out lie about it. And Bo DID lie about it. Frankly, the whole justification in the apology was contrived as well. That look of anger on Pelini's face would seem to indicate that it had nothing to do with the Missouri incident and everything to do with Pelini being afraid that the camera had caught him being an ass.
The apology allowed everyone to just put it behind them, but it did not change the fact that the behavior of both Pelini brothers leading up to the apology was less than honorable.