I think the answer comes from what Smith tells Morpheus about the original Matrix, which was a paradise. Humans rejected it, so the Machines were forced to make a more realistic virtual world.
SMITH: The perfect world was a dream that your primitive cerebrum kept trying to wake up from. Which is why the Matrix was re-designed to this: the peak of your civilization.
So originally, the Machines aimed to create a world where humans were as happy as possible. But on the second try, their goal was to create a world where humans were as happy as realistically possible. If that meant there were some computers (computers that no doubt would seem laughably ancient to the Machines), so be it.
Also, you make the point that creating a Matrix with computers in it seems to help out Neo and the human resistance. But keep in mind, the very existence of the human resistance and the One was accounted for when the Matrix was created. According to the Architect, the Oracle came up with a method where "99.9%" of individuals would accept the Matrix, and it was always understood that there would be some able to break out.
