Let me preface by saying that nothing I argue below supports particular policy positions taken, either actually or as strawman, by Harris et al..
The OP is correct that the divide about religion among "secularists", "atheists" and "liberals" is largely the divide between those who approach it scientifically and those who approach it as might be typical in the Humanities. But the OP is wrong that the Science perspective in only concerned with the literal truth of religion's cosmology. The science perspective is also and even more concerned about truth about religion's societal and moral impact, which is also a scientific question and one that Humanities is not equipped to deal with. The scientific perspective includes the more rigorous and valid elements of social science within psychology, sociology, history, and political science which converngently support the claim that at the heart of Islam are ideas that, whether the ideas are taken literally or metaphorically, promote "Illiberality and intolerance", including anti-reason, anti-equality, anti-liberty, and pro-authoritarianism.
This conclusion is supported by the most valid data and basic theories from the relevant social sciences.
In contrast the OP author's and "Humanities" perspective that rejects this claim on a scientific question of fact is, like much in the Humanities, based in emotion, political bias, made up nonsense, and active disregard for valid empirical evidence. They stake claims about empirical issues based upon "evidence" with all the same invalidating qualities of isolated anecdotes, and when they make reference to actual social science it is almost always either centuries out of date or selectively from the weakest and least validated sectors of social science. For example, they still refer to and teach Freud, Jung, and their Psychoanalysis as if their ideas were ever empirically grounded and not largely invalidated by the subsequent century of actual psychological science.
A study of 150 top colleges found that they teach an average of 11 courses that mention "psychoanalysis" in their formal course descriptions, with 10 of 11 being courses in the Humanities (and the 1 within Psychology typically is a critical and not promoting view of the practice and Freud's claims). The Humanities clings to them because they like the narrative they tell and don't care about whether they distort the realities about the actual nature and causes of various psychological and social phenomena.
The same is true with their apologetics for Islam and religion in general. They take positions on questions that are scientific and factual issues based not upon concern for what the actual answer is, but on what answer tells their preferred narrative.
The OP author unwittingly reveals the biased motives of this perspective when he/she says:
Despite all its remarkable accomplishments, Western culture feels guilty and ill at ease. It traded in God for Snooki, swapped transcendent meaning and social cohesion for a vision of Enlightenment that started out bubbly and gradually went flat, like a can of week-old Mountain Dew.
IOW, just like the liberal guilt that makes white liberal deny clear factual realities about race and crime rates in favor of an "it all due to racist cops" narrative, they deny clear facts about the intolerant, authoritarian nature of Islam and monotheism in favor of a preferred narrative that simple-mindedly blames the rainbow-unweaving and party crashing "science" for the replacing existential poetics of true art and Romanticism with crass and emotionally vacuous commercialism.
They equate the rejection of religion with a rejection of art, metaphor, and appreciation for the aesthetic features that religion shares with humanistic expression in general. That misses the point entirely, which is that the problem with religion is precisely that it asserts be more than another humanistic expression in the pantheon, but stakes claims to not only cosmological realities, but to moral and political dictates. That is what defines them as a religion rather than another work of fiction with a sizable fanbase. The problem with Abrahamic religions is that they are mostly about the evils of those who treat them as fiction, no matter how great, and that even as fiction, their central hero is as immoral and abhorrent as a villain could be by post-Enlightenment standards.