I'm waiting until TNO releases another press-release that their very smart people have found a very unique way to solve this or that problem...
It's more likely that TNO will conclude that light aircraft in flight cannot be controlled from a distance at all since they're all mechanical, and even if they do have autopilots these can easily be disabled. It's also not possible to disable for instance the engine in a non-lethal way (EM pulse or something) unless it's a FADEC equipped aircraft.
So the only way to try to stop such a potential threat has to be sought initially in warning the pilot that he's in no-go territory, with lasers, flares or tracer rounds most likely. And if that doesn't work, then there is no other option left but to deploy traditional lethal means.
And there's probably a footnote that a light aircraft has never imposed a significant threat to any warship or other military target (except for the publicity value - Mathias Rust comes to mind). The load capacity is simply not large enough and then there's the matter of detonation.
They'll wrap it all up in a nice report and present it to the authorities along with a nice invoice.
Nevertheless, there are some good things said on this thread. I have seen the documentary about the USS Vincennes (I think it was) who shot down the Iranian passenger plane. I don't know if procedures have changed, but one of the reasons for the confusion about whether the plane was civvy or not, was a lack of understanding how the civvy aviation world used its frequencies, transponders etc. For one thing, I think they used UHF guard instead of VHF guard to warn the aircraft. And they did not mention the squawk the aircraft was using.
From this thread, I hope that the military learns that GA aircraft, particularly the small ones, do not automatically monitor VHF guard all the time due to lack of radio equipment, brain capacity or whatever. So in addition to guard they should also broadcast on other likely frequencies.
I don't know if it is technically possible, or desirable, but would radio equipment that simply broadcasts on all 600+ aeronautical VHF frequencies simultaneously, be a partial solution? "Light aircraft at 3000 feet, heading 090, 20 miles east of Harwich, squawking 7000, approaching US warship Vincennes, contact Vincennes on 121.5 immediately. I repeat..."