Beyond that, the call for herem was not simply for the sake of exterminating or killing people. The Canaanites were devoted to religious practices that would threaten the worship of Yahweh (and the redemption of humanity) with corruption and error. Brutal child sacrifice, religious prostitution and so on were essential features of Canaanite religion.
The question I've always had about this part is: if the Canaanites could have been converted to the worship of Yahweh, would it have been necessary to kill them? I think the answer is "not necessarily" -- Rahab, the Jericho prositute being a particularly good example.
Using a contemporary example I would suppose that any number of Japanese in Nagasaki or Hiroshima would have been amenable to U.S. occupation, representative democracy and such. I suspect there were plenty of Germans in Dresden about whom the same could also have been said.
However, the U.S. in order to achieve victory, saw fit to fire bomb (in the case of Dresden) and atomic bomb (in the case of Nagasaki and Hiroshima) the inhabitants of those cities rather than argue the merits of the Constitution and American republicanism.
It is an analogy that can only be pushed so far - but aside from intramural discussions of the mystery of election (Rahab and her family are saved out of all others) - the analogy of wartime expediency, necessity, etc. would seem to hold some water.
Beyond simple expediency, there are examples of others in the Hebrew Scriptures who came into Israel from outside peoples, presumably converting to the worship of Yahweh, but bringing in their errors and abominations (exs. Jezebel, some of Solomon's wives). Perhaps that was a danger that 'complete destruction' of the inhabitants of the Land was meant to prevent.