We're kind of spoiled here in the US, being the world's only superpower (for now) and having been involved in several wars after WWII, none of which threatened our survival and most of which could be called "optional." That isn't normal.
For most states throughout history, survival is at stake, and when you go to war, you do so with every capability you have. Anything less and you are taking an irresponsible risk. As such, I think the more interesting question is how do you NOT justify nuclear war, or, how do you keep a conflict from going nuclear?
Going back to the original question, it's actually pretty simple. For tactical use, the justification need not be any more complex than that it's a bigger boom--more efficient and effective use of ordnance. For strategic use, where civilian casualties are a concern, just remember that in our last total war effort, WWII, cities were legitimate targets.... the factories because they produced war material... and the residences because hitting them would create "absenteeism in the workforce." It's ugly, but it's true, and even if you don't want to intentionally kill the workers it's not likely a government in total war will avoid nuking an industrial center to avoid collateral casualties. This is the reality of strategic bombing as a strategy, with or without nukes; nukes just make it happen faster.
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