I think a race that grows 9+ feet who is your enemy is reason enough to get rid of them. No need to connect a bloodline of fallen angels from Gen 6 to find motivate. I'll leave Gen 6 where it is but I don't see this niphilim race of gen 6 continuing post flood and what we see post flood is of a different blood line.That's true, the text doesn't come out and say that. But when the conquest began, some of the population of Canaan was devoted to destruction, some was to be put to forced labor, and others were merely to be driven out.
Here's a blog post (the author is a scholar) that identifies the clans containing giants as the ones to be exterminated.
Why were the giants singled out for destruction? If the angelic interpretation of Genesis 6 is true, they represented a continuing danger to humanity. The rest of the population could be kicked out or forced into slavery, but the giants had to go.
Related to this, afaik the early Jews and Christians all held to the angelic interpretation of Genesis 6. Only later, sometime around Augustine, did the human interpretations begin. For example, the 1st century Jewish historian Josephus included the angelic interpretation in his book Antiquities of the Jews.
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