If the "whole program" which fell into the hands of Al-Queda consisted of anything other than ashes left over from Thermite ignited components then someone needs to be court martialed.
EVERY military unit dealing with sensitive equipment and documents has the plans and supplies necessary to destroy those things before they fall into enemy hands. This policy goes back to artillery units "spiking" their guns if those guns had to be abandoned during an emergency retreat. Steel spikes were driven down the "touch hole" (A small hole through which the propellant charge of a cannon or muzzleloading gun is ignited) of their guns, thereby preventing your advancing enemy from turning those guns on you.
I can only hope you are right.
At this point it doesn’t sound like they disabled stuff, just withdrew to an undisclosed location?