You'd need to pick a scalable solution; where we have one drone today, we could have 20 in the same place for half the cost in the future.
In my opinion, the best solutions I can think of are:
1) EMP. May not shut off the motors, but should shut off the brains.
2) Base station with targeting system. Laser would be too slow, too dangerous. Maybe a high-powered water jet. Knock them right out of the sky. Break their wings.
3) A swarm of predator drones. Good ones would not be self-sacrificial.
I think a laser would scale much better than a water jet. Not to mention, isn't it hard to justify spraying water at every bird that flies by when you're stationed in a desert?
I think in the end, the cheapest thing will be something like a small gun mounted on turnable mount, with a camera attached. If it sees small something flying overhead, it shoots - normal airplanes will be too far up to hit, and if you have a lot of low-flying traffic, you could replace the bullets with rubber. Make certain - by physical means, not software - that the gun can't swivel below a certain angle to avoid shooting basketball players in the head.
In my opinion, the best solutions I can think of are:
1) EMP. May not shut off the motors, but should shut off the brains.
2) Base station with targeting system. Laser would be too slow, too dangerous. Maybe a high-powered water jet. Knock them right out of the sky. Break their wings.
3) A swarm of predator drones. Good ones would not be self-sacrificial.