Hmm. Legato is probably the most interesting character in Trigun. I don't know whether or not Legato has been brainwashed by Knives. I don't think so.
Legato isn't cruel or insane. One of the key points of his philosophy is that human life is all suffering. Humans are worthless and much better off dead. In destroying humanity with Knives, Legato probably believes that he is doing the right thing. He is ridding humanity of its suffering and preparing the way for the superior plant race. As far as his fanatical devotion to Knives, I could very well see how that could make sense in Legato's mind. The two of them have the same goals in mind. Knives is an immensely powerful being both physically and mentally. It would make perfect sense for Legato to follow Knives.