Regardless of the altitude, everybody seems to be forgetting that the Stinger and similar shoulder-fired SAMs use an infrared homing system. It would have latched on to the biggest heat source around and homed on to it. That heat source would be one of the four engines. Yet all the conspiracy theorists agree that the plane was hit in the fuselage. How do people explain that?
Details, details... However, if this was a missile, it provides support for a radar-guided and not an IR guided missile.
The DHL attack in Baghdad can be considered a test case for the effectiveness of a shoulder-launched SAM against an airliner.
First, the missile hit in the wing, next to an engine as would be expected of a heat-seeking missile. Second, there was no massive structural failure from the missile, instead the primary damage was caused by fire from leaking fuel. Additionally, the crew was able to maintain control of the aircraft and land safely.
Flight 800 was damaged in the fuselage so suddenly and catastrophically that the crew was unable to make a mayday call or attempt to return to land.
If 800 was terrorism, I would suspect a Project Bojinka-style bomb.
My theory is that it wasn't hit by a heat-seeking missile. It was hit by a rolling-airframe missile (RAM) that hones in on its target by tracking its radio signature. This type of missile contains a warhead that explodes next to its target similar to a WW2-vintage flak shell. The exploding warhead would then shred the target with hundreds of small tungsten-carbide cubes that cut through the aircraft as if it were made of paper.