I agree with you about the missile. *IF* it was a missile, it was likely a radar-guided, or a least terminally-guided (radar or optical) missile in order to hit center mass. AND when you add on the altitude of the strike, the scenario of Achmed with a Stinger or similar just doesn’t make sense.
ALSO, the nature of the reports of the missile track and smoke trail do NOT align to the flight characteristics of one of the US Navy’s big SM-1s, or SM-2s. So let’s leave the US Navy out of this.
I’ll go with a sophisticated attack using a radar-guided SAM
There is still the problem of the lack of physical evidence of a high-energy explosion. Now, if the FBI (in the days of Reno Justice) had said that, I could see someone's having room for skepticism; but this part of the investigation was controlled by NTSB. If the aircraft had been speared by a SAM, it would be pretty hard to miss or conceal the evidence.