Don
To get hold of someone with no chance of a 3rd party intervening and making them disappear in a way that wouldn't necessarily alert that 3rd party to then taking countermeasures in a timely fashion.Rather than thinking of convoluted ways in which they could have done it - I mean, no one's pretending someone couldn't take control of an aeroplane - what about the why? The how isn't the biggest leap of faith here... I'm yet to hear a convincing reason why taking control of this plane/hijacking it/crashing it/whatever would be a good idea for the actors involved.
Intelligence agencies/military have no real qualms of causing collateral deaths if it means they get their man.