At least one other poster mentioned EMP, which I would have thought to have the ideal capabilities for the job. ISTR a trunk-sized EMP device was marketed at police forces some years ago with the idea that it could be used to shut down the electronics, and therefore disable the engines, of cars that were being pursued. It was a stupid idea, of course—you don't want your power steering and brake servos losing their grunt on a 70mph bend—but it may be a much better fit for drones.
If you don't want to simply EMP them, and prefer a soft landing approach, I'd suggest a Goo Drone. This is a drone itself, and it's designed to fly over the intruder and dispense a couple of pints of goo that progressively hardens on air contact, in about 20 seconds, to form numerous strands of rubbery spaghetti. The goo falls in, on and among the intruder's props. The rotors don't stop instantly: instead, they gradually seize up, offering a fair chance that the drone will make a slow descent and survivable landing. (You don't want to kill a £300 drone at the expense of the $100m F-35 that was directly underneath it on the flight deck.)
For my last offering, if you want to immediately kill an intruder without too much risk to bystanding people, planes and radar masts, make a large bore shot weapon that can fire a few pounds of ice chips or rock salt or something similar, with a muzzle velocity of, say, 800 fps. The stuff needs to have a ballistic profile that tapers fast against air resistance. Get the material, grain size and propellant right and you have a weapon which would blow a drone into small pieces at 50 yds without offering the slightest threat to something 300 yds downrange. Ideal for fast-moving and manouevering close-range airborne targets I'd have thought?