Drones have the potential to cause serious damage, up to how much for one engine rebuild?
Money talks, so why not 'dissuade' ILLEGAL drone operators by downing drones in no-fly areas? There are already several options and I'm certain the military have a few more that aren't in the public domain.
Another less dramatic method would be to assign an encrypted unique identifier to each drone/transmitter combo which has to be registered. (Like the MAC for IP devices). Admittedly, this could be circumvented or spoofed but it would reduce the problem.