If someone initiates war, brings war to your people, threatens the destruction of your people (I mean as a nation state) - you are morally entitled to do anything required to defend your people. Anything. Without exception, and up to including killing every single person of the attacking nation if that is what is required to stop the war (which you did not initiate). Realistically you won't have to go that far, however there is no scenario where you can have total war on the scale of WW2, and civilians from the attacking side are not likely going to die in very large quantities. All of those deaths, without exception, rest on the moral back of those who began the war.

The attacking party holds the moral responsibility for what is required to stop them.

If you have to kill all the civilians supporting the industrial side of the war in order to stop the war machine supplies (whether in Nazi Germany or under the Empire of Japan), the moral responsibility rests with the party that initiated the war.

Your moral duty as a defending nation is not to trade your people's lives at a equal proportion so that you feel great about not killing too many people. It's to make the attacking party stop, capitulate, give up, surrender their efforts, and that is all. If that requires killing their civilians at a 100 to 1 ratio, that is entirely morally rational and just. The guilt of those deaths entirely rests with the attacking nation.

Which is also not the same as saying that the defending side should kill as many civilians as possible, just to do it. It means they're absolved of civilian deaths on the attacking side as a concern morally, so long as the civilian deaths serves the purpose of helping to end the war.