Maybe not. The hijackers would have tried to fly as low as possible toward the target, a very risky maneuver with a large commercial aircraft, and might well have hit the water. Also, the passengers might have stormed the cockpit once it was clear they had been hijacked.
I'm still going with this version: The flight was tracked across Malaysia and intercepted by the Malaysian Air Force over the Straits of Malacca. The plane was repeatedly ordered to land. Whoever was in control of the cockpit ignored the order and the plane suddenly began to turn south toward Kuala Lumpur. Malaysian Air Force pilots receive a shootdown order, to avert a possible suicide attack on KL. 777 disappears from radar. No information is released, as the Malaysian government and others are trying to figure out how to tell the story without inflicting a massive hit on commercial air travel around the globe.
Now if this happened, someone probably saw something, and the Malaysian navy almost certainly knows where the wreckage is.