We cannot read Ezekiel 9 in isolation. The preceding chapters show that God’s people had become so disobedient that they had openly adopted the practices of Babylonian religion. God’s response is to find those who still feared him and to destroy the rest, including the women and children. If that seems harsh to us, perhaps it is because we don’t take sin as seriously as God does. We also don’t like a sovereign God who offends our sensibilities. But if God is God, he does not “owe” us another chance any more than he “owes” us a long life or even another breath.
God takes his Word so seriously that he will sternly judge his people when they turn away from him. Remember that judgment begins at the house of God (1 Peter 4:17).
If unbelievers have trouble with this, then they aren’t ready yet to become believers. We needn’t spend time trying to “defend” the Bible. We don’t need to “defend” Ezekiel 9 or somehow excuse what God did here.
The God of John 3:16 is also the God of Ezekiel 9.
See God’s Word Has Not Failed.