My two cents worth:
A lot of our fans are always saying that no player is ever bigger than the club, or should ever be undroppable at United. I agree with this, and because of that I think far too much is being made of this.
Lets be honest, Ferguson and co know far more about tactics and conditioning than any of us ever will. We were playing superbly for the first hour, and whatever set-up they had envisaged for this was clearly working. I'm a big Rooney fan, and personally I feel that he could have replaced any one of our front four and performed at least as well on the night, but we aren't paid to make these decisions, and Ferguson got it right.
Regarding Rooney's temperament, I think that Ferguson realises by now that he might be on those players that needs a reminder every now and again of what they represent here. With Wayne, it usually occurs after an incident. Perhaps this time, given the circumstances, it might simply be some pre-emptive, clever man-management.
Unless there is a major red flag that we aren't aware of, we'd be crazy to let Rooney go.