Sam Harris and the limits of empiricism

Everyone, particularly Sam Harris, is very excited about creating a new science of well-being. Surely, Sam Harris argues in his new book, science can tell us facts about what actions and policies lead to human flourishing, and what lead to suffering?
Science allows us to measure people's well-being levels. We can scan their brains, we can measure their heart-rate, we can see the effect that, for example, meditation has on their pre-frontal cortices. We can see what therapeutic interventions leads to a reduction in the symptoms of depression. So we no longer have to go round and round in interminable debates about morality. Once we accept that morality is principally about the wellbeing of conscious beings, then we can leave it to empirical science to give us the facts and clear up this whole morality business, right? Take it away, science!
But here's my problem: I don't think outside observers can ever really know what is going on inside someone, or can say with objective scientific certainty that this inner subjective state is 'flourishing' or 'suffering'.
A great deal has been made about the fact that neuroscientists have discovered that advanced practitioners of meditation show more activity in the pre-frontal cortex than novices. But so what? Who's to say that greater activity in the pre-frontal cortex is 'good'? Why is it good? On it's own, it's just another part of the body. Standing on your head increases blood-flow to the brain. So what? We'd still need to see how a person lives, how they use their pre-frontal cortex, whether it enables them to live better. Is it possible that someone has a very developed pre-frontal cortex, and is still a bounder?
You could use other physical correlates to assess someone's well-being: their physical health, their longevity, their heart rate and so on. But that only tells us if someone is a healthy animal, it doesn't tell us if their life has any meaning or purpose. It is very difficult (I would say impossible) to measure a life's meaning empirically, and yet a genuine sense of meaning and purpose is probably one of the most important aspects of well-being.
This much is more or less admitted by Martin Seligman, father of Positive Psychology, which claims to be a 'science of well-being'. Seligman says that the Good Life is composed of three components: the pleasant life, the engaged life (or 'flow'), and the meaningful life.
Seligman says that science can definitely measure the pleasant life. More on this shortly. It can possibly measure the engaged life, if you define the engaged life as those moments when we become totally absorbed in what we're doing - although there are serious philosophical problems with this definition of well-being, as I have argued here.
As for the meaningful life - a life animated by a sense of higher purpose - Seligman admits this is very hard to measure empirically. He says: 'Meaning is assessed by some combination of societal judgement, factual consequence and subjective state'. How ever would this work in practice? So far, science has not been able to provide any sort of objective measurement of a life's meaning. And it would be somewhat horrifying if it could. Imagine the eulogies at a funeral: 'Jimmy had a good life. Yes, admittedly, he only measured 4.6 on the Seligman Life Meaning Index. But still...a good try at the good life.'
The other great pillar for the new science of well-being is questionnaires of subjective well-being (SWB), which ask people how happy they are. But there are all kinds of problems with these questionnaires and the data they provide. They only really measure pleasant feelings. They don't distinguish between higher and lower types of happiness (they take the Utilitarian position that instances of happiness differ only in intensity and duration, in which case, would Keith Richards' life on smack be considered the best life?).
They rely on a person's own assessment of their happiness - and a person might consider themselves to have high levels of 'the good life', when everyone else might think they lived a wretched life (or, alternately, they might consider themselves quite wretched when everyone else thinks they live a deeply meaningful life). We might think we're happy and blessed, when everyone else thinks we're not. Who's right?
Harris usually uses the example of women being forced to wear a burqa in Afghanistan to show that western scientific societies have made a lot of moral progress and that we now 'know' that this is a brutal and barbaric custom, because it leads to the suffering of conscious creatures.
OK, the Taliban is a pretty uncontroversial example to pick, and I'm not about to defend them. But what about, say, Turkish women's desire to wear headscarves? Is that also barbaric? What if they want to wear headscarves? Should they be allowed to decide for themselves what leads to their wellbeing, or must they obey whatever western science tells them is good for them? After all, as Harris points out, science isn't democratic. If it is a 'fact' that headscarves are bad for wellbeing, then sorry girls, off with those headscarves!
To take another example, Sam Harris is a big fan of meditation (despite being a sworn opponent of religion and insisting that religion has nothing of value to teach science). Now if he came across the Buddha fasting and meditating under a tree, completely socially isolated, his body dangerously weak, and apparently in some sort of coma, Harris and every other western scientist would probably say: 'By every empirical measurement this man is causing himself physical damage. He appears to be trying to kill himself to achieve some delusional state called 'Nirvana'. It is the obligation of science to save him from his misguided life choice and to set him on the path of wellbeing, which involves a healthy diet, a good job and a rich network of friends'.
Empirical science could not understand this person's life choice, because it was so different from what empirical science tells us typically leads to well-being. The only justification for the Buddha's life-choice is within, in his own ground-breaking vision and his own consciousness, and outside observers could never measure that or turn it into empirical data. Many scientists would still say that the Buddha was wasting his time and should never have left his cushy position as an Indian prince.
'Yes', you rejoinder, 'but western science is accepting more and more of the Buddha's insights'. OK, let's take a more extreme example. St Simeon Stylites, the Christian ascetic who lived on a pillar in Syria in the fifth century AD. He was a filthy, flea-bitten, isolated, starved, sunburnt hermit. By no scientific measure could he be said to live a 'good life'. And yet he probably had more sense of meaning, purpose and agency than any of us. And, if you believe in God and the after-life, as he did, then perhaps he really did live a good life, in the sense of a life dedicated to overcoming the ego and devoting oneself to God. But a man in a white coat and a clipboard would shake his head at St Simeon, and probably try to lead him away to the loony bin.
In fact, how many of our great moral leaders would be committed to the insane asylum today? Mohammed, the Buddha, Jesus, Abraham, Socrates - all of them heard angelic voices, so according to empirical science, they were all suffering from schizophrenia.
The point is, science can only tell us the mean, the average, the common. Harris tells us that science isn't democratic, but when it comes to the 'science of well-being', that's often exactly what it is: little more than a show of hands, or a survey of customary responses to the question 'what makes you happy?' It tells us the average, not the virtuoso.
Harris claims science can show us the various different 'peaks' of human flourishing, but the whole point about peaks is that they are often hidden from ground-view. Sometimes you have to scale them to see them. Peaks are lonely places which few people reach. From an observer's point of view, how would you recognize a peak when you saw it? How would you measure it? How would you know it was a peak, unless you could look inside a person's soul?