Joshua was instructed to exterminate all Canaanites. One group, the Gibeonites, tricked him into making a treaty.
So he didn’t kill them, just enslaved them and their descendants. They were much later slaughtered by King Saul.
I think it’s also relevant to point out that in the ancient world few people were really “free” in the sense we use the term. They were enmeshed in webs of obligation and duty, even if not in legal servitude. The actual condition of women in most societies differed little from what we would see as slavery.There were also intermediate conditions between slavery and freedom.
So slavery was not viewed, probably not even by the slaves, with the horror we view it. It was just a fact of life, one of the bad things that could happen to anybody that was unlucky.
Jude Wanniski described this as the Mommy Party and the Daddy Party and that people were attracted to each as they saw their advantage there.
One other item that I think about, particularly when God orders someone killed, is what was their conversation with God? Had God warned the Canaanites for generations that they needed to move, that this was not and would not be their land?
We live in a world of lost knowledge which the Scriptures repeatedly emphasize. It is obvious to us in our modern world that a lot of knowledge gets lost.
Opening Stanza from Choruses from "The Rock"
The Eagle soars in the summit of Heaven, The Hunter with his dogs pursues his circuit.
O perpetual revolution of configured stars,
O perpetual recurrence of determined seasons,
O world of spring and autumn, birth and dying
The endless cycle of idea and action, Endless invention, endless experiment, Brings knowledge of motion, but not of stillness; Knowledge of speech, but not of silence; Knowledge of words, and ignorance of the Word. All our knowledge brings us nearer to our ignorance, All our ignorance brings us nearer to death, But nearness to death no nearer to GOD. Where is the Life we have lost in living? Where is the wisdom we have lost in knowledge? Where is the knowledge we have lost in information? The cycles of Heaven in twenty centuries Bring us farther from GOD and nearer to the Dust.
T. S. Eliot (1888-1965), The Rock (1934)