If one word just becomes a halo word for all good feelings and the other a word for all the evil ones, then the distinction becomes more propagandistic or polemical than real.
Sure, as we usually understand the words "patriotism" is a better thing than "nationalism," but it's also more of a luxury of long-established states secure in the world. Nationalities that are still struggling to become independent and countries that are less secure and less powerful are always apt to be more "nationalistic."
I don’t think that you meant “nationalities” are struggling to become independent, you meant, nation states. Let’s hope that it is not nationalities.