That is an extremely vague statement, but is basically a statement of the logical positivist notion of the scientific method which is now universally accepted as inadequate. The philosophy of science and the scientific method is a very complicated (and unfinished) subject, and crass statements like this just won't cut it as serious claims about the nature of scientific investigation. If you're interested, the Standford encyclopedia of philosophy gives a good overview of some of these topics (or pick up a copy of "Criticism and the Growth of Knowledge," or look at http://en.wikipedia.org/wiki/Demarcation_problem)
> I'm sure in your scenario we'd want to know the reason why intuition works so well (and there would be a reason)
Yes, if in that scenario we knew the reason intuition worked, that might make it rational to use intuition. But a method could be effective even if we didn't know why it worked, and you did not add in any additional criterion of "knowing how it works" in your original statement. Are you sure you actually meant what you said?
Regarding the moral issue, you seem to be suggesting that (1) reduces to the fact that humans have a preference for not killing people (as far as I can tell, your vague references to "parts of the brain lighting up" aren't doing any work here, they're just decoration). But of course we all recognize that moral statements are different from statements about preferences -- they are descriptions of what people /should/ do, not what they like to do -- so I don't see that there is a successful reduction here. (Unless you are willing to be a moral nihilist and believe that there are really no facts about what people should do, only facts about what they prefer to do.)