The one thing missing in their calculations is how they know the locations that the plane was hit and crashed. Looking at the footage, there is no way in hell the jet traveled 8km between getting hit and crashing (even based purely upon the size of it in the camera as it falls). With a very rough calculation, I believe that an object of that size should appear to shrink by about a factor of 6 if it travelled from 2km away to 10km away (from the observer). The Russians gave very different locations to the Turks last time I checked (the Russians' estimate was actually a much shorter distance).
Their calculations are very simplified; assuming the plane was travelling in a straight line and continued to do so after being hit, and that it didn't slow down at all (due to either air resistance or the engines cutting out) and so on. From the footage, you can clearly see that it goes into a nose-dive, which is exactly what you'd expect. That alone means that the engines are providing their thrust pushing towards the ground and the wings no longer providing lift to keep the aircraft aloft (another thing the physicists forgot), and so it crashes into the ground not very far from where it was hit.
Following on from that, given that there would have been increased acceleration towards the ground from the momentum and thrust of the aircraft, we can safely assume that the aircraft was at a higher altitude than they estimated, as it would have fallen further in the same amount of time.
So, whilst their calculations are mathematically sound (obviously), they are based on simplifications and incorrect analysis of the situation.
What we actually learned from this, is don't simply assume that because something involves maths and comes from an academic source doesn't mean it's correct.