> Our current conception of a "drone" is really hard to bring up to military spec once this sort of countermeasure becomes militarily common.
This isn't really for drones. It's for frying ground-based electronics like cell phones. Drones are the smoke screen to hide that fact.
As for drones, motors and batteries are quite hardy against quick microwave pulses. A bit of aluminum foil makes a good, light Faraday cage. Optocouplers can isolate radio and GPS modules from the actual motor control systems.
I would expect you can fry an RC drone, but an autonomous one operating inertially or capable of switching so when radio/GPS goes away is probably pretty easy to shield.
In addition, this kind of system is always going to have a range vs width tradeoff. Can the drones get inside this thing's range where they can still be effective even if they are "ballistic"?
Dumb old bombs are really effective if you just give them a little bit of GPS to improve their accuracy. You don't have to get very close for the GPS adjustment to be devastatingly effective.