Lets assume the drone is more or less blind to whatever happens above it as most of its sensors are pointed down and being stealth reduces its need to be aware of other planes (and forbids active radar). It should be feasible to approach it without being noticed and somehow entangling it (a net?) on its return flight, slowing it down (a parachute) until it runs out of fuel, and do it while jamming its communications so its owners won't have a clue of what's going on.

I think the worst problem is detecting it in the first place.

Getting back to the actual focus of my comment -- the original article leaps to "obviously, the Iranians have broken our encrypted controls" from an Iranian press release, without bothering to give even speculative support. I consider it far more plausible that something simpler has happened, such as dumb old software failure, or GPS spoofing.