I personally think the entire book of Joshua is not a factual account of history, very little information outside of the Bible supports it's claim. Treating it like a historical document that can be disproved is nonsense. The scientific article this started on wanted to discover what happened to the Canaanites, and only mentioned the Bible to say it was one of the few records of the period and that they were exterminated in it.

On the other matter, the Bible states that extermination is the goal, and describes the campaign to do so in detail. That it later says there may have been pockets they missed doesn't mean Bible scholars are making the entire thing up.