Just posted the same question but nobody seems to know.
Problem is the pilot not the [engine off] command. Ai pilots tend to start the choppers automatically. They make noise and waste tons of fuel. Altough they never take off automatically they sometimes do some taxiing.
If you do a [engine off] command and then kill the pilot with a setdammage 1 everything is fine again. But nothing else seems to work, neither ejecting them nor disabling AI move. Im really stuck at this and currently I do the "setdammage" thing to get around this...