When someone in the Bible does something evil against someone else (like the Babylonians decimating Judah and Jerusalem), and it is serving the purposes of God, does God hold it against them (the Babylonians)?  Actually, this question was asked by a teenager to which I immediately said, “good question!”  

The Bible records many instances when God uses Godless unbelievers who are immoral to be used to get the attention of his people.  What we see in these instances is Godless people doing what is natural for Godless people to do and God choosing not to intervene or protect his people from their evil.  So, the short answer is “yes,” in spite of the fact that God uses their “evil” for His purposes (chastening leading to repentance), they (the Babylonians) still will be held accountable for their actions when they stand before God.

This is all part of the reality of the sovereignty of God.  Somehow, he takes the actions of all people, weather good or evil and is able to include all human decisions to accomplish his divine will/plan for humankind.  Nothing happens that surprises God and nothing can derail or even slightly impair God’s plans for the world.  Everything fits perfectly into his design…that’s amazing!