How about some powerful green lasers, which effectively make a transparent 'wall' in the path of the aircraft. It wouldn't stop them if they were intent on being there, but it would show the pilot that there was something going on, and that they were somewhere that they shouldn't be.
Not sure if green lasers can be made powerful enough yet to be daylight visible? Person operating them would need to be sure that there was nothing higher up either....wouldn't want to blind the airline crew that's up higher!
Or as suggested above, a 'wall or red flares' would likely achieve the same effect.
Finally shooting some non-lethal weapons (eg flares, plastic bullets, etc) at the aircraft may cause it to use the prop, or engine. The aircraft would have to ditch, but provide those on board with some chance of survival, compared to simply sending a missile at it.
dp