What Ragged said.
Destroying airplanes is a good way to get very very angry attention from the Corporate Court's underlings, local, national and international authorities. Just have a CC Justice on the next plane he decides to bring down. Not only will there be magically active security on the plane, but the follow-on investigation will make sure that, if he lives, your player has very little interest in pursuing such tactics in the future.
If you don't want to have quite that much hell rain down on him, reduce the CC Justice to a Senator, or witness for the prosecution in a major case. Then, it won't be quite so likely that they'll kill him as soon as his spirit appears in the plane.
Besides, if he's done this more than once, as Ragged said, there should now be magically active sky-marshals on flights in the area, scanning astral space around the plane.
Oh, talk about a brain fart, at 30,000 to 50,000 feet, he's dealing with at least a Mana Ebb -1 to -6, your discretion as GM), and given that Shadowrun planes tend to go into the upper-most atmosphere, if not break it for transcontinental and intercontinental flights, it may even be a Mana Void (-7 to -12), see Street Magic, pg. 119. Most of that range is enough to reduce your player's spirit to low force, if not out-right suppress it completely.