I'll go by what I've learned working for the Air Force for the past 20 years. The odds of the government sucessfully shooting down an airliner, and covering it up for 10 years are almost nil.
The airplane would have had to shoot down the airliner, then land at another base than it took off from and be rearmed (if it used a missile, the missile would have to have the same serial number as the one fired), and then it would have returned to it's original base.
Now, this would have to be done in such a manner that no Air Traffic controller would ever discuss the fact that the fighter was given instructions to divert to another base, no ground maintenance crew would ever discuss the fact that he refueled or rearmed the fighter jet (or even saw an unknown aircraft land).
Oh, and this would have to be coordinated in a matter of minutes, so that everything could be put into place so that the fighter could land, shut down, be rearmed, and take back off, and land back at it's original base without anyone wondering why it took an extra long time..
Oh, and to add one other thing...they'd have to figure out a way to explain why the plane was gone for, say 3 hours, but the engine monitors only show that they were running for 1 1/2 hours to the ground crews at home station.
And, none of that would match up to the reports by various pilots that when they took off to intercept the planes, some of them had ZERO munitions on board, and that they knew that they may have to go all Kamikaze to take down one of the airliners if necessary.