In other words, they would have had to have been in the most favorable launch position, directly under the course track of the aircraft and linearly somewhere on a line slightly in front of it to slightly behind it. It would depend on the seeker sensitivity of the missile - if it could lock on from a slightly forward aspect angle. That would be best, then the missile could fly nearly straight up. From slightly behind, the seeker gets a better look at the hot engine exhaust, but has a slightly longer tail-chase intercept.
I don't remember the specifics of the witnesses that claim to have seen a missile trail. Here again, if I remember correctly they thought they saw something arcing in, not climbing straight up. The other consideration is, why was there only one?
Think about it, put yourself in the planners position. You're a terrorist organization, and you want to shoot down an airliner, strike a blow, etc. You're going to go to all the trouble of setting this up... Why shoot only one missile? They are not that expensive. If you can find a source to get one, you can probably get more than one. A big 4 engine aircraft might just shake off a single small missile hit. Heat seekers go for the engine exhausts and fragment. 747s fly very well on 3 engines... We may hate terrorists, but don't assume they're stupid just 'cause they're fanatics. Something the size of a 747 I'd shoot at least 3 at it, figuring 1 to miss, and needing 2 good hits to have a fair chance of bringing it down - giving the pilots too many problems to cope with in time. I don't recall any of the witnesses described multiple missile trails.
I don't think anyone can definitely prove there wasn't a missile (hard to prove a negative). But examining the data it looks extremely unlikely.