> Or perhaps he was just evil and had a hatred of humanity that he was justifying with whatever reason pleased him.

For me. Agent Smith isn't coded as evil. He represents the cold rationality of the scientific algorithm - "I've been studying your species...". He's simply curious. It would never occur to Smith to "justify" anything, even to simulate pleasure. Smith represents what Kant called the limits of pure reason - the ability to measure, compute and model everything, but understand nothing.