I don't think it was the bench that hurt AC Milan yesterday at all. It was the goalkeeping. There is no way that Dida should have given that much of the near post to Rooney in extra time. If he has his angle correctly, that is an easy save for Dida. The first goal by Man U was a gift, Dida either had to commit fully to punch the ball out or stay on his line and hope for the best. He came out half way and stopped. He's too tentative. I am sure I need not remind everyone of the goals he let in against Bayern (he flinches and looks *away* from the ball for the first one and let's the second one beat him near post). Milan are playing with fire giving up goals like that to a quality team like Man U.
THEN, when the score is 2-2, Milan could not get out of their own half (it seemed) and the defense was under constant pressure. In a big game, you can't go into a defensive shell like that or you are bound to get burned. The easiest way to avoid being scored on is by playing in the other team's half as much as possible (IMHO).
I agree that the loss of Gattuso significantly affected AC Milan's ability to get the ball out of their own end, but a part of me wonders if AC Milan were sort of content with the 2-2 score (nota bad rsult for the away team). Nevertheless, the team now needs to step it up and win at the San Siro. AC Milan has done it before and hopefully they have two more in them.