Wino, you might be comparing apples and oranges in discounting the missile theory completely regarding TWA800.
There are missiles and there are missiles… Everyone here is talking about heat seeking missiles that, if absolutely accurate, will hit a target's highest IR signature. (I can't comment on whether that would be the jet exhaust or the aircon pack outlets on a 747.) Most, but not all 'lightweight' missiles, (the shoulder-launched varieties) fall into this category. (Military aircraft use flares to avoid such missiles.)
Then you have your active or passive radar homing missiles. (Most of the bigger, more sophisticated surface to air missiles fall into this category). Either guided by a ground station or using their own radar guidance systems, (or a combination of both - ground station guidance until within short range of the target, then switching to their onboard seekers for the final homing), they will seek out the largest radar signature - the centre of the cruciform - where the wings meet the fuselage. (Military aircraft use chaff to avoid such missiles.)
Getting back to the IA A310, it's interesting that no official report seems to have followed this pilot report. You would have to hope that if there's any basis to this, a Notam would have at least been issued for traffic overflying Somalia. To say that authorities and airlines know this incident has occurred and have ignored it is stretching the conspiracy theories beyond my comfort levels. Just surmising here, but if the incident did occur, my guess would be that some warlord's clan launched an old SA2 or 3 unguided within sight of the IA crew. (I'm told by friends unfortunate enough to have seen one, that an SA 2 launch is quite spectacular and guaranteed to concentrate the mind if you're in an aircraft within sight of it.)
I wouldn't have thought it would take a rocket scientist (no pun intended) to launch such a weapon (ie, simply 'light the taper' and stand back to watch the fireworks). It would be a very different matter to set one up with all functions operational, acquire a target and track it properly and then launch it for a successful engagement.
If the incident did occur and authorities are apparently ignoring it, I'd say it's because they know that this was just someone pickling off an old missile to watch the fireworks or impress his friends. I may be wrong, but I do not believe an SA 2 launched this way could acquire and track a target after launch - unless God was really trying to tell you your time has come.