Can't you go around that if you have direct line of sight to the drone, with some laser or very targeted radio? Or perhaps a relay drone. Also I assume the drones will increasingly become autonomous.
For what it's worth, this attack can be sidestepped fairly easily just by not using open frequencies, to which microwave ovens are usually tuned(for regulatory reasons). This is only useful against drones that are available to buy for individuals, as they are forced to use the same open frequencies. Anything military grade is likely using other frequencies, and you can't use cheap microwave ovens to generate ridiculous amounts of them.