what is the difference, morally, between a shooting at a draftee or a civilian?

The difference isn't their status (draftee vs civilian). It's being an armed combatant. That's the moral difference - whether the individual poses a threat to you and your mission. If the guy on the other side of the line has a gun, shoot him. If not, take his surrender. Kinda like: "if wearing helmet with 'wrong'-colored tape, hit; else not", only in the real world.