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The behaviors described by Veritatis Splendor as human acts cannot be attributed to God, because His acts are divine. The peoples of the land of Canaan were wicked and opposed to God. Israel was His instrument of judgement on the peoples of the land of Canaan. Their actions were ordained by God to cleanse the land and to protect Israel.
If a judge sentences someone to be executed, the executioner is not committing murder. If the judge sentences a group of people to be executed, it is still not murder. The scale does not matter. With human judges, the motives may be questionable, but with God, the motives are always right.
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God makes plenty of commands that are recorded in Holy Scripture. Why would Deut. 20:16-18 be an exception?
The original Douay-Rheims translation of Deut. 20 prefaces this chapter with
Lawful wars are to be undertaken with courage and confidence.
The war is lawful because it is defensive. It is to defend the people against the great spiritual threats of the idolaters, whom the Lord knows would tempt the people of God to violate the 1st Commandment.