My guess would be either some form of IFF/SSR failure on the airliner or the TOR itself and if I had to guess I could see the following sequence happening - The IRG operator saw an object not squawking any Mode 3A/C/S idents (the codes which say "hey I'm an airliner") and told his Battery Commander who, when unable to ask for higher clearance (am I being Jammed?) and under the immense pressure of thinking that this unknown object may have been part of a US retaliation, made the ultimate decision to shoot.
Again, pure guess work on my part but based on knowledge of the region and the types of equipment used etc.
Regardless of the "How?", the IRG would have known what really happened as soon as the Battery Commander was finally able to report what he did, and the Government would have known shortly afterwards, my guess would be at most it took 24hrs for everyone in a position of authority to be briefed.