I neither disagree nor agree with Harris (see my post for what I actually think), but I don't think you've understood the argument sufficiently to refute it. I'll pretend to be Harris and counter your arguments:
1) Scientific inquiry elucidates all facts that are available to our perception. Morality is a perception, therefore science can study it.
2) Yeah, so? Science doesn't force us to be moral - but it can tell us what is moral and what is not. The scientific psychopath would know that his behavior was immoral, and wouldn't care.
3, 4) Science will discover whether or not those humans are correct to believe that that course of actions is moral.
Read here: http://lesswrong.com/lw/fv3/by_which_it_may_be_judged/ to get Harris's viewpoint, stated more articulately
1: Harris compares pursuing moral goals to pursuing health and claims they are fundamentally similiar (i.e. both part of the basic purview of science). This is what I'm disputing here.
2: See the reply I've made already, both here and my other argument.
3: Harris could claim that a question of the worth of animals could be solved by checking the brains of humans, but this begs questions of why human brains are the only ones that are taken into account. In addition, human brains are likely often contradictory on the subject- a law of averages could be used, but why is it so valid?
4: Harris claims all morality is about the well-being of conscious creatures. That's what I'm objecting to here.
Sam Harris is here offering a substantial amount of money to anyone who can show a flaw in the philosophy of 'The Moral Landscape' in 1000 word or less, or at least the best attempt.
http://www.samharris.org/blog/item/the-moral-landscape-challenge1
Up to $20,000 is on offer, although that's only if you change his mind. Whilst we know that this is very difficult, note how few people offer large sums of money for the privelage of being disproven.
In case anyone does win, I will remind you that this site is created and maintained by people who work at MIRI and CFAR, which rely on outside donations, and with whom I am not affiliated.
Note: Is this misplaced in Discussion? I imagine that it could be easily overlooked in an open thread by the sorts of people who would be able to use this information well?