»Zion is a slave world.«

I disagree with the mwm theory.

Still, Zion is not free, just like Smith said to Neo.

There is a 1% anomaly that if left unchecked would crash the Matrix. Therefore the 1% needs to be removed from the system. That means that if Morpheus et al werent rescuing the 1% from the system, then the system would crash.

So then, Zion actually serves the Matrix' best interests. They are still its servants, they are still its slaves.

In fact, the Architect tells Neo that they can destroy Zion easily: they have become increasingly efficient at doing so. If they can destroy Zion at any time, then the fact that it existed for so long points to the fact that the machines have allowed Zion to exist.

So why do agents fight the hackers? Why not let them do their thing? They are a security feature of the system. Even though the hackers serve the system as well, the hackers cannot be allowed to roam the system at will because they are still a part of the anomaly that would crash the system if allowed to accumulate.

When the One reboots the system, Zion isnt needed anymore, and it gets destroyed, and then rebuilt again.

This is brought up in depth at