There is circumstantial evidence of a coverup. There were a lot of U.S. Navy vessels in the area. And a terrorist's missile didn't have to be a man-portable missile if it was mounted on a boat. For example, the SAM-6 is a portable self-contained radar-guided system and a single missile must weigh a few hundred pounds. Not man portable but easily portable in a small powerboat (launching it would be no picnic, but these are people who don't really care about getting burned alive by rocket exhaust). It would easily take out any commercial airliner. The warhead must be several kilos of high explosive.
I think you are correct that, at the very least, an IR SAM would have taken out an engine and maybe broken a wing, but it could not have cracked open the airplane and left no opportunity to declare an emergency.