My club does one of these every year. It's safer than at least half of the ordinary flying that goes on every day. The target is low and slow and on the far side of the runway, and if it's disabled by a shot I'll just chop the throttle. So far, it's been hit quite a few times, with only cosmetic damage. The plane we use has solid balsa sheeting on the fuse, and while a paintball can punch a hole in the sheeting, it will be liquid by the time it gets to the interior of the plane, so It can't damage the control system.

If you want an absolutely safe sport, there's always checkers. Shooting paintballs at a plane is probably a lot less dangerous than things like driving to the flying field.