I'm not sure how much RC modeling you've done, but the drones are radio-controlled. You can't harden a radio-controlled device against microwaves. These days, radios utilize frequency-hopping technology, but that can't prevent jamming.
These things should be designed so that they can't be jammed and they can't be damaged by a microwave beam weapon.
These are controlled by two means: Radio and GPS. You can't prevent jamming or being shot down by a microwave without spending millions of dollars to harden the equipment and encrypt the communication.
You can harden a radio against microwaves. It's not even hard.
Jamming is also only a problem if you remain in range of the Jammer. If you know where the jamming bubbles are, it's not great feat to program the drone to fly far beyond it's range and then reacquire a control signal within some radius of your drop point.
Also, I wouldn't rely solely on GPS for navigation. I would use the GPS, but I would give an inertial navigation system outvoting rights over the GPS. They can spoof GPS, but they can't spoof your inertial movements and orientations. Use inertial guidance to get your gross location, and when the GPS and inertial approximately confirm each other, you can switch back to GPS for accuracy.