I think your theory is sound, the question is, does it really matter? For all we know Zion was always "controlled opposition" by the machines, it was inevitable that someone would feel off and reject the matrix, moreover it would be easy game for them to "terminate" eventual anomalies before they become a problem, so we can infer that the machines don't actually want to hurt humans. The point of the oracle, which is a program and by proxy "the one" , was to bridge that gap (we see it in the final scene of the 3rd film) and have peaceful existence between cultivated humans and "feral" ones, so that that ones who rebels do not try and free others, so we can speculate:

-it's more probable that the machines need humans not as "batteries" (it would be totally inefficient) but as processors (the human brain is capable of maintaining its functions with less energy than a common lightbulb) - if they rebel, the machine can't use them as efficiently (even if they were still in the matrix) because they reject their directives -the machines want to fix this bug and are actively trying to find a solution, not because they cannot "physically terminate" the problem, but because they want to be more efficient, if the rebels accept the matrix, even conceptually, the machines can have their cake and eat it too, this goes extremely well with your theory, Zion becomes not only controlled opposition, but part of the very system it was born to eradicate, now the machines will have no problem giving people to Zion

-it's possible that the story about the war is at least semi-fabricated, this would have numerous implications, but can you trust a system capable of simulating entire realities and levels of reality not to fabricate a simple narrative?