While I very much doubt that the decision to shoot it down would be taken while the jumbo jet is still far out over the ocean, or if the government was convinced that this was the old fashioned "Take me to Cuba" type hijacking, I am certain that as a last resort measure the jet would be shot down.
No one is going to take the chance that the jet will slam into a major building or a crowded sports stadium -- not after 9/11.