sky9, I must confess I have not yet read the entire report but isn't your suggestion of an extra 2 or three tons a bit arbitrary?
If the destination is tempoing (= change of up to one hour) thunderstorms then perhaps carry an extra one hours holding. If, in addition, the alternate is also tempoing the same then best find another alternate with better weather.
Flying around in such weather without a lot of extra fuel puts crews under enormous pressure and, I believe, this accident is an example of what can happen. The crew and, in particular, the captain have all my sympathies and it was fortuitous that all came away unscathed.