Holy Schnikeys!
First, the crew of the United 737 does not seem to have done anything wrong. He was cleared to take off and did. There isn't enough information available in this animation (and the rest of the factual matter doesn't seem to be on NTSB's website), so it can't be determined whether the failure is the controllers', or the Atlas 747 crew.
This doesn't really matter, though, this business of right and wrong. In the worst accident ever, a runway incursion, the pilots of a Pan Am 747 were relatively blameless, and the pilot in command of a KLM 747 acted recklessly -- to the detriment of all in the KLM plane and many in the PA bird.
Second, if the time hack on the CVR is nominal, this did not happen during daylight, as depicted, but at three o'clock in the morning. There are two interesting things to note about that. A) it's dark and hard to see stuff and make out that a moving light in the distance is a threat, and B) this is the absolute low point in the circadian rhythm of any person adapted to a normal day shift.
Other than that, all I can say is... wow.
By the way, here's the direct link to the NTSB animation.
http://www.ntsb.gov/Events/2006/MostWantedFed/AnimationDescription.htm
d.o.l.
Criminal Number 18F
A friend and co-worker lost his father in that KLM collison. I remember when he got the call at work telling him his father died in that tragedy.
When the 747 first came out, the pundits were railing about the possibility of such a great number of fatalities should two 747's collide in mid air. Now we have a new twist with terrorism and the new Airbus 380. (If it ever gets built).
Imagine if a terrorist "sleeper" became an ATC. They wouldn't need a martyr or a bomb. One person making a "mistake" like this would be all it takes. Another timed attack using multiple sleepers could be the next 9/11...
Watching it was one of those "This can't be happening" things.
One good thing about 0300 was the 737 was probably near empty, allowing him to fly over the 747.