Judges 3.2 describes, God left those nations simply because He wanted to teach the subsequent generations of Israelites, who had not experienced the earlier battles, how to conduct holy war.
The idea of holy war is not a very positive one today. While it’s quite an old concept the Muslims have made the idea immensely unpalatable. The Muslim version of holy war involves using women, children and the handicapped, in addition to men without other options for gaining heaven, through the means of suicide, for accomplishing their objectives. Their holy war is the destruction of the infidel or the conversion of the infidel through terror and fear. The god they serve is abusive, terrible and unattractive in every way. Yet holy war predates Islam.
The Jewish God used the term holy war to describe the movement of His people from slavery to freedom by disbursing the nations who lived in the Promised Land. While God gave these people 400 years to repent they became instead increasingly more offensive to Him until they were condemned to destruction at the hands of the Jews. While God did indeed command His people to remove the occupants of the Promised Land the Scripture records a dismal record of success. Not because God was or is incapable but because His people were faithless and disobedient.
The holy war God describes really wasn’t a war of weapons with mass human destruction. The real war is one of faith and obedience between ourselves and God. While God called Israel into the Promised Land the cause of their victory would be God Himself through the miraculous, through nature and through the Israelite army, winning the war.
The first battle Israel was to win was the battle over their fear and doubt about God’s calling and commitment to Israel. When Israel believed God and subsequently obeyed God, they found success. The win was sometimes at their own hand like David and Goliath. The win was sometimes at God’s hand like with Gideon and his small band.
Jesus, God as man, fought His holy war before beginning His revelation of Himself as God, the Savior of the world. The great enemy of God, the devil, engaged Jesus hoping to cause Him to doubt His mission and to disobey His mandate. Fortunately for all of humanity, Jesus prevailed.
This too is the holy war Christians must wage today. They must overcome their fear of the world, and their lack of faith in God’s goodness in order to wage war against every argument and idea that pits itself against the knowledge of God in any place. Christians are to war against their own will by embracing the will of God to love and serve all humanity until all of humanity experiences the love of God through them and invites the Savior into their own lives as Lord of all.
There is still a need for holy war, not the Muslim kind but the Christian kind. One leads to death the other to eternal life.