Yeah, I wonder what Smith had planned for Zion. He tortured Morpheus hoping to get the codes for Zion’s mainframe. Perhaps that would have been enough; just take over and shut down the life-support machines.
I sort of like Robot Chicken’s take on the subject:
<fx Egon voice> It would be… bad. </fx>
Not to hijack, but I always thought Smith was after the codes for Zion’s computer not to destroy Zion, but so he could escape into it. He talked about he hated the Matrix. I thought he wanted out, and he saw this as his way out. That’s why when he was interrogating Morpheus he removes his ear piece, which cuts him off from the other agents.
The agents watch Mr Anderson for awhile, and then move on.
ETA, that’s considering the first movie only.
No, he didn’t hate the Matrix, he hated how humans smell.
Yes, he literally says that.
I just figured all the Agents were out to find/destroy Zion, but Smith had started to make it personal.
Smith may have had extra desire to attack Zion, but, prior to Neo going inside of him, he didn’t have a choice but to do what he was designed to do. Neo gave him the choice to go rogue.
Since Zion is just the haven that the machines let the humans have as a release valve, I don’t think Smith would be allowed to destroy it. It has to remain until the One is found.
The video game The Matrix: Path of Neo offers this hypothesis.
As for what that means for the rest of the series, your guess is as good as mine.