"...every bomb short of a nuke would be perfectly legal to shoot into a mass of afghan civilians), and the commander giving that order would go completely free under international law."

Um...no. The Law of Armed Conflict (LOAC) (internationally recognized and codified in US statutes) states that those making the attack must take into consideration proportionality. A commander who orders an attack that kills 50 civilians just to get one terrorist will be punished for failure to adhere to the LOAC.