If God's command to Saul in 1 Samuel 15 was exhaustive - if God was commanding a genocide, then we would expect the Amalekites to be wiped out. After all, Saul is only criticised for taking plunder, not for sparing them. He thinks he obeys Samuel's command (1 Sam 15:20).
But that's not what we see. In 1 Samuel 27:8, there are still Amalekites around for David to raid. In Esther, Haman seems to be descended from the kings of the Amalekites. They weren't wiped out, therefore God didn't command a genocide.