While the military may still be somewhat competent, I would be absolutely shocked if they made the effort to jam any and all signals this thing was sending to its controllers as that would have involved signal jamming on an large scale as well as potentially attempting to interfere with non rf communication methods as well
Theatre-wide jamming would have been ‘spectacular’ eh?
Foot stomping here, but there may or may not be assets that can ‘interrupt’ or ‘spoof’ the link from the “object” to the various relay birds.
We will never know, most likely, exactly what was done and how.
From my experiences of working with the .mil folks, I am pretty confident they handled this well. Civilians? No.
The least likely solution would be something to ‘jam’ the transmission, be it RF or another manner, of a moving object in the stratosphere for at least 3+ thousand miles. However, the installed package did apparently have both RF receiving capabilities as well as solar cells, the two weakest avenues to provide an overwhelming energy source to disable the onboard systems.
Other options get a bit more fanciful, but fully shielded systems are such a rarity that they’d be options for also disabling the onboard systems. Easiest to take out the radios or batteries.