I think you've simply mischaracterized Harris here. He's not justifying evil actions because their rational - at least, from what I've read from your citations. So, your thesis seems to (wrongly) assume that Harris thinks because some evil person is rational, his actions are "better" than the irrational (albeit benevolent) person.
Moreover, I don't think it's correct to say that rational people do stupid things. In everyday language, "rational" and "stupid" are antonyms. Based on your essay, what you're trying to say - I think - is "rational people do evil things." And you're right. Hitler and Osama are perhaps the most rational people. But to conclude that this diminishes the value of rationality is to simply commit a logical fallacy: There are people who are evil and rational. That doesn't mean everyone's who's evil are also rational, vice versa.
It's like saying knives are murderous weapons in themselves just because you've seen someone being bludgeoned to death by a knife.
Finally, one of your commenters is right. "Intellectuals and supposedly rational people also fall for the same bias when letting their emotions get to them." That's an argument in favor of rational thinking. You're attempting to argue that rational decision-making can sometimes lead to very undesirable (but not necessarily moral) results. I don't think this is theoretically tenable.