It would be fairly easy to simply disallow people from spawning on the end of a runway if someone is there. You'd get a message like "traffic on the runway" or something, until the little spawn area is clear, perhaps forcing you to spawn in a hanger if you're impatient.
To prevent idiot friendlies from sitting on the end of a runway and blocking traffic forever, you could simply give people about 15 seconds or so to get out of the spawn area before they are forcibly "de-spawned" back to the tower. The spawn zone would be simply a small square on the end of the runway. So if you were getting ready to up with a bunch of squaddies or something, you could just spawn, then taxi off to the side and wait until everyone is out.
Then again, you could just leave friendly collisions off and forget about the whole thing. I'm pretty impartial to either idea. Maybe do it for ToD and leave collisions off in the MA, since friendly fire will be on, with no killshooter, in ToD.
You might even go as far as allowing only hangar spawns.