How I Would Do It
I would have mounted a precision rifle (12mm caliber) in the second seat of a Mig25, looking downwards. Then acquire the drone while overflying my territory optically, fly over it with the Mig25 and put a bullet through the jet turbine. That will disable thrust and (hopefully) make the drone glide to earth with some damage sustained. But assuming the drone does indeed have proper gliding characteristics, the resulting wreck could easily be what we have seen in the video.
Disabling of the jet turbine could be trained using commercially available engines for executive jets. Surely different parts of the engine will show different failure modes.
Then of course I would tell the world I did it electronically, to make sure my approach will work again in a future requirement.