How’s obliterating Amalek different from Arab Jihad?

Question: If we are commanded by Hashem to kill Amalek, then how is that any different then the Arabs who claim that Allah told them to kill Jews?

True the concept of erasing Amalek, today, sounds cruel. On the other hand, the eternal Torah, had to be relevant not only today, but 3300 years ago, as well. To judge methods of national survival 3300 (!) years ago with a modern measuring-stick is anachronistic and simply irrelevant. The same loving G-d who commanded us the super-moral mitzvot, also commanded us peace-loving and “slave-mentality” Jews who just left Egypt, that sometimes we must “toughen up” to “fight fire with fire” in self-defense and retaliation, and is the same G-d who historically “lost” Amalek somewhere along the line, because He doesn’t want that “mitzvah” to be preoccupying modern man. He made sure that Amalek no longer exists, but the only thing that remains is the obligation, once a year, to remember that sometimes we “nice guys” who would do anything not to kill, have to artificially “get tough”, otherwise our anti-Semitic enemies will surely take advantage of us (it still took us thousands of missiles down south until we finally retaliated!). Like a loving Father teaches his naive daughter not to let others take advantage of her. Self-defense, retaliation and deterring the enemies of peace is life-giving and moral, and the exact opposite (!) of Islamic terror which brags about how many innocent citizens they killed, and even names their streets after those evil “heroes” of terrorism. The world has difficulty understanding why the Arabs in Azza could be the aggressors, if they consistently suffer more casualties, because thank G-d, the world doesn’t understand the mindset (and illogic) of religious Jihad!