Just like the better researchable Assyrians the Neo-Babylonians employed this as a proven tool to assert their control of the conquered lands and the remaining people there.
Once the head of the snake is removed, it is no longer needed to crush that head?
The Assyrian policy of deportation is analyzed as
punishment for rebellious behaviour;
liquidation of ...
I'm going to guess you're coming at this with the idea in your head that every living soul in the country was exiled. That's incorrect.
In fact, while the Bible itself isn't consistent on the subject (and its our only real source), most likely what happened was something much closer to your "I could understand" option. We know the exiled included ...