It says that resources were depleted when the bombs fell but in spite of this in places like Appalachia you can create machinery to harvest resources at claimed workshops.
Granted, he didn't pull the trigger, Emil Pagliarulo said he wasn't a war criminal, and described that event as being 'one of the horrors' that Nate saw in war.
What if one of the horrors, as Emil said, was Nate finding out how dismissive he could be to the loss of life?
Maybe part of the motivation for his good actions in-game could be that he wants to be better.
It says that resources were depleted when the bombs fell but in spite of this in places like Appalachia you can create machinery to harvest resources at claimed workshops.