I think that would work better in The Animatrix; putting it in 3 would be a tonal shift, plus a sudden human victory would feel a bit Mary Sue or Deus Ex (ironically) Machina to me.

But in The Animatrix, you could get away with that, plus we can see the early attempts at utopia that Smith described. Perhaps something about how utopia for some people didn't work for others could be illustrated with an auto-antonym on some load-bearing part of the dystopic-utopia?:

  Some believed we lacked the programming language to describe your perfect world.

We can see this even in current discussions of fiction, where people look at e.g. The Culture and see a dystopia, while famously many of the powerful in tech are parodied for taking the wrong lessons from fiction with "At long last, we have created the Torment Nexus from classic sci-fi novel Don't Create The Torment Nexus".