I've always thought the probabilities were the following (in order):
1) The Malaysian Air Force splashed it, fearing another 9/11 in Kuala Lumpur. No government will talk because they know what release of the truth would do to air travel.
2) Some variant of the author's/General McInerney's theory - the pilot killed the passengers and stole the plane, flying it to a friendly country through some trickery or another.
3) The Diego Garcia theory - he got too close and the USAF splashed it.
4) The Southern Ocean theory - for public consumption.
Your #3 is on my possibles list also.
#2