Just war theory dates back to when people were fighting with swords and arrows. It applies no matter what the weapon is. If civilian areas of Tokyo and Dresden were specifically targeted (and I do not know that they were) yes, that would have been immoral. You cannot deliberately target civilians in war. Period. End of story.
Is a farmer whose crops feed the army a civilian? Is the truck driver bringing that food to a port a civilian? Is the owner of a small machine shop in the midst of a residential neighborhood, one who performs one operation on a critical component of an important instrument of war a "civilian?"
Merchant seamen? Logistics officers? Nurses? Anyone whose efforts support the ability of the "combatants" to wage war?
And then what of those forced to fight? Those who, if it weren't for the political officer at his back, would go back to his home or desert to the other side?