I'm hopeful someone equally knowledgeable writes a rebuttal, as most of us don't have the technical ability to know what flaws might exist with this theory.
Most conspiracy theories become "conspiracy theories" because they fail to pass Ockham's Razor. For example, there's a good 3000 words there about how but exactly fuckall about why. Meanwhile, the "how" skips over how three decidedly nondescript Georgians managed to disable a 777 with 230 passengers on it all while managing to spoof Inmarsat.
On the other hand, a demonstrably incompetent organization losing two airliners to tragedy within six months seems unlikely so we assign nefarious agents to the problem. Nefariousness, to our thinking, is more probable than dumb chance for the simple reason that we can protect against nefariousness.
I mean, if the Russians wanted to send a message, they'd send a fuckin' message. 007 was the second airliner the Soviets shot down and they really didn't much give a fuck. Are we somehow saying Putin is less belligerent than Yuri Andropov?