Missing dimension: the Gibeonites’ appeal to Joshua. None of the other Canaanites were of the same mind.
There was an earlier promise of driving out the Canaanites supernaturally, which was rescinded due to the disobedience of the Hebrews in the wilderness.
Also, Haman in the book of Esther is described as an Agagite, which shares the name of one of the kings of Amalek.
Do you believe the children of Amalek and the children of Jericho deserved to be slaughtered?