Virtual Reality - your first point is wrong, which means the rest of your train of logic is flawed. Even if the aircraft was on 'minimum fuel', reserves for a 777 are typically only about 3 tonnes. If flying around above minimum reserve fuel leads to this sort of accident then I think Boeing are in big trouble.
Somebody mentioned excessive water warnings in the fuel tanks. I know BA have been checking all the 777 tanks for water. They are getting lots of warning messages but not finding any water. The problem is the unreliable water sensors, not actual water in the tanks.