A much more apt comparison, to begin with, would be between siding with humans or cows being used as food – because that's what humans are to the machines, a way to stay alive. Second, humans have proved time and time again that they can't be trusted, going as far as ruining the entire planet in fear of the machines – WHO WERE TRYING PEACEFUL NEGOTIATION, mind you. Thirdly, despite not really needing to do so, the machines chose to minimize human suffering, even in the horrible position forced upon them. Ideally, I'd want them to collonize other planets and abandon Earth, if possible, but otherwise I'd be fine with them having a crack as the dominant species over humans.