If they went to this much trouble to steal the airliner, they’ll also keep the passengers alive as hostages.
Be prepared for the jet to show back up with them onboard, happy to be released, but a question if the jet is now an assymmetric WMD. With the passengers on board, there will be incentive not to shoot it down, but to allow it to fly somewhere with controlled security.
Taking this to the next diabolical level, with a little careful handling and controlled environment, the passengers could be the WMD. MERS