This theory keeps coming up, but it doesn't make much sense.
If your goal is to acquire a working Boeing 777, on a secret airfield somewhere in Western China or Eastern Kazakhstan (see this map for orientation: http://www.airliners.net/uf/109874/phpnIOEWi.jpeg), then you don't have to be particularly smart or rational to realize that hijacking a commercial flight from Kuala Lumpur to Beijing, with 240 people on board, and then attempting to stealthily cross both India and Pakistan, as proposed in the OP, is not your best option.
This leads me to wonder if maybe the cargo was the target. We already heard that the manifest has not been released and that they left 50 seats empty to compensate for the weight.
If your goal is to acquire a working Boeing 777, on a secret airfield somewhere in Western China or Eastern Kazakhstan (see this map for orientation: http://www.airliners.net/uf/109874/phpnIOEWi.jpeg), then you don't have to be particularly smart or rational to realize that hijacking a commercial flight from Kuala Lumpur to Beijing, with 240 people on board, and then attempting to stealthily cross both India and Pakistan, as proposed in the OP, is not your best option.