There is absolutely no reason to fly for seven additional hours to crash into water if you could do that minutes after taking off at Kuala Lumpur. Water is not in short supply there, and it's the same water everywhere.
All the available hints point at a government operation. So far, it appears to be flawlessly executed. One possible goal is to obtain an unregistered, unaffiliated airplane, masquerade it as some other civilian flight, load it with bomb(s), and send it to some other country with a suicide pilot, most certainly under a carefully selected false flag. A US airplane attacking Israel, for example; or a Chinese airliner exploding in New Delhi. It could take a while to figure out who was actually responsible - and, with proper supporting actions, the missiles would be flying by then. The World War I was started with just one shot from a revolver.
I would not be surprised if one or more other aircraft are stolen in the future after all the furor dies down and everyone goes back to normal.
Flying to the remotest part of the region possible before going in is called preventing closure.
I believe we are entering the most dangerous period since WWII, and the world is clearly and very quickly going to hell. While hoping I am wrong in this case, I expect the worst.