 Only if they refuse must they be physically killed.A few authorities have ruled that the command never included killing Amalekites.R' Samson Raphael Hirsch said that the command was to destroy "the remembrance of Amalek" rather than actual Amalekites; the Sfat Emet said that the command was to fully hate Amalek rather than performing any action; and the Chofetz Chaim said that God would perform the elimination of Amalek and Jews are only commanded to remember what Amalek did to them.