If the machines needed a power buffer for their nuclear plants, they could certain mass produce lithium ion cells. Or if they really needed a bio-battery, they could use cows, which wouldn't resist so much. Or they could simply remove the parts of the human brain that cause trouble. Put every human in a persistent vegetative state by physically destroying the part of the brain that controls consciousness.
The one and only conclusion you can draw from this is that if the Matrix is a battery bank, the machines are idiots. Clearly, judging from the remainder of the script, they are not idiots. They are, in fact, quite clever. So in order for the humans to believe the Matrix is a battery bank, they have to be the idiots. They can't just be ignorant of non-human batteries, because they exist inside the Matrix program, and Morpheus actually shows one to Neo.
So the AIs would have to perform a physical surgical intervention in human brains, inserting an autonomous microsurgeon robot attached to the Matrix connection hardware that is constantly identifying the neurons activated by the concept of a computer CPU, and those activated by the concept of the human brain, and physically removing and blocking any connections between them. The Matrix connection hardware is much more precise than an fMRI, and clearly, the machines are capable of doing fine microsurgery into the human brain to install it in the first place. The Matrix-born humans then have to connect the concepts in a way that routes around the physical block in order to understand them at all. So the humans are like batteries, but they provide a different kind of power than electricity. What kind of power? I can't tell you, and even if I could, you wouldn't be able to understand it, because the machines have deliberately damaged that part of our brains. The freeborn humans of Zion actually gave us the battery metaphor, that is as close as we can physically get to understanding what the Matrix is for.
Morpheus even says, "Unfortunately, nobody can be told what the Matrix is. You have to see it for yourself." If you are told, the physically enforced agnosia kicks in, and you are physically incapable of understanding what you hear. If you ever do manage to make the link, a microscopic pair of scissors inside your skull snips an axon or two, and you immediately forget it.
That's the only retcon I can come up with that doesn't make the whole battery concept sheer idiocy.