I personally think Zion is actually another Matrix-like world. The architect spoke plenty on the problem of choice. And he also hinted at their solution...to provide humans with the illusion of a choice. This choice is whether to accept the Matrix, or to not accept it...the red pill, or the blue pill. However it is just that, an illusion. Because Zion is still a part of the Matrix system, while they believe they have a choice, they, in reality, do not.
This is supported by The Architect's little line "this will be the sixth time we have destroyed it (Zion), and we have become exceedingly efficient at it"
Obviously they have done it a few times, and they can only destroy a city once...
Also the fact that Neo can stop the Sentinels in a strikingly similar way to the way in which he stops bullets...
My thoughts anyway.