The launch of such a missile would have been impossible to miss at night, yet none of the witnesses saw a launch. Why not? Then there's the fact that we know the back end of the plane would have climbed, yet IIRC none of the witnesses report a missile track followed by another streak rising from near the impact point.
The "missile track" was the flaming aft fuselage, surging upward after being freed from the weight of forward fuselage.
First, it wasn't night. It was twilight. Second, in order to see the launch you have to be looking for it, and it has to be distinct from the rest of the ascent. Motion, however, catches the eye. Isn't it obvious?
Finally, no one I know who isn't associated with the cover-up thinks a striken plane or any part of it will climb significantly. The government actually claims the plane rose after the explosion. I talked to the Eastwind Airlines pilot who was staring at TWA 800 when it exploded from a position just above it. He told me he didn't see anything go up. He effectively said the same thing on the ARTCC frequency. There are transcripts available if you care.
ML/NJ