The Bible presents the acts of God in destroying the firstborn in Egypt, the Amalekites in warfare, and the Canaanites as a display of His glory, i.e., His exalted beauty to be admired. It displays His love for His people before the nations, and shows them that God's favor rests upon the people who belong to His covenant.
So when atheists and liberals present it as something ugly and of which all Christians ought to be ashamed and denounce, they are recasting it into their own narrative. They want to imagine that this is about one group of people seeing themselves as superior and more righteous than another group, and so justify the taking of their land.
But as I have argued, this is an act of divine judgment by God upon a people for whom He waited thousands of years, and then another 400 years after He promised to give Abraham's descendents the land, in order that He might not judge them too quickly for all of their sins.
And in the process of that, He saves His people who would certainly have come to their end in Egypt, according to the story, their end on the road to Canaan, according to the story, and their end in the land of Canaan, again, according to the story. If one wishes to critique that story, or just disbelieve it, that's fine; but he needs to be honest and present the only text relating the actual historical reasons for the conquest.
After the LORD your God has driven them out before you, do not say to yourself, "The LORD has brought me here to take possession of this land because of my righteousness." No, it is on account of the wickedness of these nations that the LORD is going to drive them out before you. It is not because of your righteousness or your integrity that you are going in to take possession of their land; but on account of the wickedness of these nations, the LORD your God will drive them out before you, to accomplish what he swore to your fathers, to Abraham, Isaac and Jacob. Understand, then, that it is not because of your righteousness that the LORD your God is giving you this good land to possess, for you are a stiff-necked people. (Deut 9:4-6)
God then goes on to tell them that He'll do the same to them if they end up filling the land with the same evil that Canaanites did--thus arguing that this is not a matter of one people being greater than another in and of themselves, but rather that it is a matter of judgment upon one group and giving a chance of life and preservation to another to whom God has promised life and preservation.
Now, that's the biblical story and reasons for the flood, the plagues, the conquest, etc. If you want to read that in a deconstructionist manner and suppose that those are only justifications for such an act, that's your prerogative, but to conjecture another narrative and reason for the conquest is not based upon any ancient text or tradition relating the event. It's just based on a postmodern skepticism of every detail that sounds too good to be true or too bad to be justified in light of our modern attitudes. Such an enterprise is purely ahistorical and ideological in nature. That's my only point.