Rabbi A. I. Kook offers a different interpretation of these events. He says that Moses cannot himself wage war with Amalek, because Moses, the greatest of all prophets for all time, sees the course of history in its full eternal context for all generations to come. Moses therefore understands that every “force of evil” – even, and especially, the egregiously pernicious Amalek – has its own unique function in the world. Specifically, the world needs Amalek to serve as an antipodal opposition to the Jewish people, the adversary with whom they are in eternal conflict. The Jewish nation needs that never-ending conflict for their own proper development.
Because Moses understands so well the positive role of Amalek, he cannot destroy Amalek, and, in truth, he cannot even enter the fray with the Amalekites. This is a known problem with over-developed thinkers, who, because they see the positive aspects of the enemy so clearly, find it difficult to fight the enemy.
And so, instead of fighting Amalek himself, Moses appoints Joshua, who wages the war at a considerably lower level, and is thus able to defeat Amalek.
But still for the same reason, Moses, even up on the hill, is fully aware of Amalek’s historical importance, and cannot keep his arms raised. To defeat Amalek now, he must “lower his stature” by sitting on a stone, so that the nearby forces – who represent not all the generations of eternity, but only the pragmatic exigencies of the present moment – will come to support his hands. And this is the only way the Jews can have the victory.
The Jews’ faith here is thus much weaker than it could be (Moses’ hands are held up for him on either side, because he has no strength to hold them up himself). With only that limited faith, Joshua cannot completely destroy Amalek, and only “weakens” him.