Using missile to shoot down an airliner ought to be made impossible. It may be a lack of imagination on my part, but I can’t think of a circumstance where a military force needs the ability to shoot down civilian aircraft. There aren’t a lot of manufacturers of surface-to-air missile systems, regardless of their level of sophistication and range – shoulder launched or vehicle-mounted – so changing those designs to prevent civilian shootdowns ought not be a big deal. Admittedly there are many more means of bringing down aircraft beyond SAMs, but not a lot of them have the reach to bring down cruising airliners.
Civilian airliners have carried IFF transponders since World War II, so there’s the infrastructure in place already for the identification of non-military aircraft. Furthermore, it’s a violation of Article 37 1.c of the Geneva Conventions to pretend you’re a civilian – that is, it’s a war crime with all the international condemnation that goes with that, so it’s reasonable to make weapons that refuse to down aircraft that identify themselves as civilian.
So, why is this still happening?