Sorry, Rabbi, but I have difficulty with your previous point. The Torah is eternal, every single letter from it, therefore is impossible to say that something there is directed only to the Midbar’s generation. Firstly, as far as I’m concerned we do are obligated to exterminate Amalek nowadays, and we only don’t do it for practical reasons, like shibud malchuyot, lack of the Sanhedrin and so on. Secondly, the Amalek question is much deeper than only self-defense and national survival. I’m sure the Rabbi knows the famous Midrashim regarding this question, and also that he is familiarized with all the Chassidic and Mussar masters said about the message of the war against Amalek and Amalek’s essence in our lives.
You are correct that the mitzvah of Amalek wasn’t just for the midbar generation, but for as long as they exist (Shaul and Shmuel lived centuries later!). On the other hand, all (!) of the poskim agree that the special laws regarding Amalek only apply to the biological (!) Amalek which everyone agrees cannot be identified and does not exist today. Just as the laws of slaves only applied when you had a slave (in order to be relevant 3,300 years ago), and doesn’t detract from the eternity of the Torah. Ask any of the rabbis from which you learned, and they will explain that all of the important mussar and Chassidic “vortim” which we say about Amalek, are simply drashot (parables, not to be taken halachically), and should not be confused with clearly-defined Torah mitzvot (m’d’oraitah) about killing children, which was necessary in the primitive world, to deter our enemies. For example, our internal "Amalek" (problematic tendencies) obviously does not obligated us kill our own children or burn our own house! Even R. Chaim Soloveichik, who innovated the idea that aside from the biological Amalek, there is the ideological Amalek (those wishing to obliterate Am Yisrael), explicitly agrees that this should bring us to “toughening up” to fight them, but has nothing to do with their children or pets.