Yeah originally they were meant to be using the humans for computing power, there's some hangover of that, like how the agents can jump between people and some other thing I can't remember right now. Even in that scenario I think it makes sense they're adapting around imprisoning humans. The Animatrix shows the humans as being the aggressors in the war and the machines initially wanting peaceful coexistence. Initially making the matrix as a paradise seems like a benevolent thing to do.

Morpheus already in his explanation tells Neo that they really don't know much about the pre-war time, him being wrong about the Machines motivations makes a lot of sense, especially given the film trilogy shows us that even the machines themselves have conflicting beliefs and priorities and the series is ultimately concluded by a ceasefire, that the machines are willing to accept.