Starting to look this way. Could the Malay Govt be covering up the fact that they took this plane out, because it was a security threat (hijacked, full of fuel, heading for KL)??
You can almost rule this out for the following points:
1) Having an interdiction of this kind is a very messy event. There will be repeated comms challenges, fighters being scrambled, fighters challenging the flight crew (even if no reply), firing warning shots, and then finally shoot down.
2) All these will be done in air traffic radio frequencies and emerg freq such as 243mhz and 121.5. There will be a lot of aircraft that will hear these calls.
3) The determination of that it is a rogue aircraft, scramble aircraft for intercept, attempt to force down and finally shoot down will take a long track. It should also be very visible. Trust me, no one would want to shoot down a commercial airliner unless absolutely necessary and that would mean that it is reaching a no-penatration line.
4) Finally, a shoot down is really messy. And there is no silver bullet. Despite what you think about modern air to air missiles, they are not that fantastic. Where do you want the impact point, left or right engine, fuselage, etc. You are very limited in controlling that, unless you use guns.
I think I'd better stop with these details. I would like to kill speculations on this part because if this kind of scenario gets to the families, it'll just hurt them more.
PS: To add a point. If it is really this scenario, the govt would now be showcasing the reasons for the take down and not cover it up. Post 9/11 era, the logical explanation would be to minimise collateral damage on the ground, etc and painting themselves as possible victims whose hands were forced by the ones who commandeered the aircraft.