They did think it was a missile. That's why they were there in the first place. The whole event was being investigated on the assumption it was a criminal act. But as the investigation continued, it became quite clear that there was no overt criminal act. On the topic of Lisa Perry's recollection of the evening, here is some other things she claims to have seen...
"Then a moment later there was another explosion, and the plane broke jaggedly in the sky," says Perry. "The nose is continuing to go forward; the left wing is gliding off in its own direction, drifting in an arc gracefully down; the right wing and passenger window are doing the same in their direction out to the right; and the tail with its fireball leaps up and then promptly into the water below. The sounds were a huge BOOM! – then another BOOM!"
This description came from a person who was no closer than 15 miles from the crash site. I've been a professional pilot for the last 15 years. I will tell you without even a reasonable shadow of a doubt that someone 15 miles away from a 747 cannot descern the nose from the tail, nevermind the left wing from the right. Passenger window?!?! Not a chance. This lady is a liar. Plain and simple. She is absolutely not a credible witness to support any theory.
If your quote from the "courageous" Reed Irvine is really only a week old than he is about 2 or 3 years out of date. The NTSB eyewitness data has been available for years.
Finally, if you repeat something you know is not true, you are lying. It doesn't matter where the lie originated from. You don't have to believe me. Read the eyewitness testimonies yourself.
I think this guy is credible. He was major flying in a BlackHawk at the time.
Why would he lie?
Why should we not believe what he says he saw and yet believe you when you where not there and saw nothing.?
Why should we believe you and the people who agree with you and not believe him and the other eye witnesses who general agree with him and what he saw.