Or imagine a smaller system integrated on a humvee that can destroy electronics in anything along the path a few dozen meters in front and in a smaller side/side area. That'd end the IED threat from anything other than a purely mechanical IED (not sure if many of those are around anymore, as everything assumes electronics will work nowadays).
This is why IEDs are so effective in asymmetric warfare. They are cheap and anyone can get parts =(
The first time I saw the results of an IED blast was a day after I arrived in Iraq. I had to shake a tree in order to retrieve the trousers of the guy who blew himself up planting the thing. That happened a lot. Making IEDs isn't very hard, but making a lot of them without eventually blowing yourself up is.
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.