One thing that probably never happened before was the combining of the avatar (neo) and a program (Smith). They are now linked in the real world such that Neo has some control over the programs running in the real world and Smith can "brain-dump" himself into a human in the real world.
So -- that means when the size of Zion reaches a certain point its destruction is inevitable. I think maybe Col. Sanders choice to Neo is a form of control over the anomaly (Neo) as he stated. Neo sits back while the real physical threat (a large Zion) is destroyed and they allow him to repopulate it with a small number. He eventually dies off and the matrix is reloaded running smoothly until another anomaly arrives.
If Neo does not take the easy way out then he can cause more disturbances and further weaken the power grid (they stated that since Neo arrived that Zion was filling at an increased rate). So the machines option would be to destroy Zion and everyone influenced by Neo (maybe nearly everyone) and shut down their much of their systems until the population was restored.
In a way the people in Zion are like symbiots on the body (matrix) removing anyone that sees through the matrix and can therefore disturb it (by awakening more minds).