I agree with your first sentence - accidents are usually caused by small problems compounded over time.
In this case, however, I can't imagine a situation where a small fire causes enough damage to render all communication equipment useless, incapacitates the crew/passengers, but doesn't cause the plane to crash for another 6 hours.
I don't like conspiracy theories because they require many people to keep quiet (people aren't very good at that). But in this case we are left with many scenarios that range from improbable to nearly impossible.
It is usually what we cannot imagine that brings down a plane, like a DC-10 loosing all hydraulics over Iowa.
It could come down to a Sherlock Holmes axiom, after you eliminate the possible, the impossible must be the answer.