I don't see how anyone can make conclusions just from a couple of games. I also can't see how anyone can simplify the meaning of football down to the fact that a team beating another fully justifies them being better.
I'll be the first to say that last season, AC Milan were by far the better team in the final. But we had the passion and drive at the end - and that won it for us. Even now, I wouldn't say that the current Liverpool side is better than Milan's - but its getting there
Also, you have to look at the background details. We have played an extraordinary amount of games and we couldn't afford to risk losing our best player to injury (Gerrard had a knee problem). Sissoko had to be substituted early due to a horrendous tackle thus affecting our game plan. Benfica are also having off field problems so maybe the Champions league was something they were thriving upon to ease the other issues. Also, we're doing ok in the league and domestic cups unlike Benfica and had our minds on that. Its also especially difficult to retain a European cup having won in it in the fashion we did last year

.
I'm not going to use these as excuses but what I will say is that football ain't so simple - especially in a game of such importance.
Football is much more than some random stats collated over the years. Form doesn't always count - look at Arsenal-Real for example.
I'll have to admit that I'm not Mourinho's biggest fan - but thats because of the rivalry with Chelsea. Other than that, I rate him a lot. Contrary to belief, its not easy having a multi million pound team. There are the pressures and expectations, and I think Mourinho has handled it well. Its also difficult to maintain a team's hunger when they are winning so regularly. Also, the way that he fits in and improves players (i.e. Joe Cole) is highly commendable.
Although they lost yesterday, Mourinho has shown his brilliant tactics and motivations skills in nearly getting a result from a nearly impossible feat. 10 men against arguably the best team in Europe + Ronaldhino ain't easy. Sure, he constantly moans and sometimes his teams can be boring to watch - but he gets the job done and there is no hiding his talent.
I rate Rafa higher tho :p