I didn't see this thread until after I posted in the other one, but I've thought more about the non-linear power requirement idea, and it solves all of your problems quite well.
If power required per unit speed increases with speed, this means that commercial craft will have lower fuel consumption than military craft almost by definition, as they rarely run around at the same speeds. Missiles, on the other hand, will need more power, and thus more fuel, for a given speed.
I'm not sure of the exact formula to use yet. Simple drag equations say velocity squared, but that seems a bit steep.
Another concept borrowed from naval architecture is hull speed. Simply put, a longer hull has less resistance than a short one for a given speed (all else equal). Apply that to Aurora with weight instead of length, and suddenly big commercial ships are more efficient, while small missiles are less so.