I don't know a lot about cycling, and only really started watching the Tour last year whilst I was unemployed, so what I'm about to say probably goes against some unwritten rules of racing.
Why should one man (Cancellara) decide whether or not that the stage should stand as a race? From what I could see, he has some clout as both a senior rider and the (then) holder of the yellow jersey, so having a word with the commissars isn't a problem as such, but I do think he was told to go slow because his team leaders were involved in a couple of the crashes. Tough!
Can you imaging the uproar if (and I'll use the F1 comparison as most people are familiar with it) Jenson Button went off on the first corner and had to pit for a new nose-cone, whilst Hamilton backed the pack up and McLaren told everyone to not pass him until Button had got back on track and joined the group?
What's the point of having a race, if teams then decide (and pretty much force the hand of the commissars due to the riders actions) to nullify a section?
I'm with Hushovd on this, times and points should have been left to stand. It's the riders own fault that they didn't bother to compete especially over the last 20km where the roads were largely dry anyway.