I'm not sure that in an article such as this, the author needs to draw any such distinction because the difference in the two situations is perhaps what he considered to be self-explanatory.
But thats the problem. You and I see the difference; the writer is the one who equated them. According to his distinctions, a German citizen could not morally cooperate with the Americans to overthrow Hitler nor could he act against Hitler on his own. I'm not sure thats what he would mean to say had he thought it through.
The whole issue of "just war" is seldom going to be entirely clear cut, and in any conflict you'll find good people in disagreement with one another as to what is right and proper, but this writer hasn't attempted to draw the necessary distinctions. He has I think falsely equated the two cases.