There is evidence that some intellectuals have some underlying moral motives in investigating the existence of God. In his recent comment, Schumacher quotes Aldous Huxley:
I had motives for not wanting the world to have meaning; consequently assumed it had none, and was able without any difficulty to find satisfying reasons for this assumption....The philosopher who finds no meaning in the world is not concerned exclusively with a problem in pure metaphysics; he is also concerned to prove there is no valid reason why he personally should not do as he wants to do. For myself, as no doubt for most of my contemporaries, the philosophy of meaninglessness was essentially an instrument of liberation. The liberation we desired was simultaneously liberation from a certain political and economic system and liberation from a certain system of morality. We objected to the morality because it interfered with our sexual freedom.[In his comment, Schumacher attributes this quotation to Ends and Means, 1969, pp. 270, 273. I have not verified the citation.] Although I have not checked the original source, it doesn't seem too much of a stretch to interpret Huxley's meaningful/meaningless dichotomy as akin to theism/atheism.
Putting aside the absurdity of trying to support a generalization with anecodotes, we can dismiss Schumacher's interpretation of this quotation. Schumacher's original essay was about why atheism is more prevalent among contemporary scientists than the general populace. Huxley is not contemporary, and he was not a scientist. Schumacher has a larger thesis, though, that atheists in general believe that no God exists only because they wish to escape its (sexual) morality, and they persist in their disbelief in spite of what ought to be rationally persuasive evidence. Again, this quotation fails to support his thesis. Huxley specifically asserts that he "was able without any difficulty to find satisfying reasons" to support the assumption* of meaninglessness. Huxley asserts reasons that appear to be independent of his desire to escape sexual morality. Huxley says that he investigated the question of meaning because of his desire for "liberation", but he specifically contradicts the idea that the direct cause of his actual belief is this desire.
*Huxley appears to be using "assumption" here in the sense of "hypothesis".
Huxley's predisposition to finding meaninglessness seems to bias his investigation. But an a priori bias does not necessarily fatally compromise the search for objective truth. The actual reasons an investigator finds to support an hypothesis stand on their own, regardless of his bias. Our task as scientific investigators is not to eliminate bias, but to recognize it and try to overcome it. I haven't read Huxley's book, and I don't know what the specific reasons he found to support the idea of meaninglessness, so I don't know if his reasons really are good, if they stand on their own regardless of his bias. But I do not know that they are bad, either empirically or philosophically. All I know is what's been quoted: Huxley says he has found reasons to support his conclusion, which contradicts Schumacher's thesis that atheists consciously ignore good reasons that undermine their conclusion, that atheists disbelieve in the existence of God because — indeed just because — they wish to escape theistic sexual morality.
But how far does Huxley's predisposition really bias his investigation? All morality involves a tension between what we want and what is "right". So any moral investigation is biased by what we want; if what we want were exactly congruent to what is "right", it is the same thing to say we're doing it because we want to or we're doing it because it's right. And, at least me, the distinction between what we want and what is "right" is vacuous. I don't worry whether or not it's "right" to eat food and drink water every day, live in a house, read, see a movie from time to time, work, study, etc. I do these things because I want to. It's a reasonable position to say that if I want to do something, I will do it unless there's a compelling reason to the contrary. So when Huxley says he wants some sort of sexual freedom, he is doing nothing but moving this desire into the domain of moral discourse. If he didn't want it, he wouldn't worry about whether or not it was "right".
If a rational, sensible person wants something such as sexual freedom, and someone tells her that this sexual freedom is "wrong", then the first thing she is going to do is investigate the reasons for the prohibition. The first thing she will do is look for direct natural reasons. Does the exercise of sexual freedom, for example, conflict with her desire not to hurt anyone? Does it pose an unacceptable risk of disease or death, conflicting with her desire to live a long and healthy life? (In a related example, I would prefer, ceteris paribus, to smoke cigarettes inside my house. I know, however, that second-hand smoke is harmful, I do not want to harm the people I share a house with, and therefore I don't smoke inside.) If there are persuasive natural reasons not to do something, then, as a rational person, I am not going to do it. Simply denying natural reasons because one wants to do something is profoundly irrational.
Lacking a direct natural reason, she will then look at more indirect social and legal reasons. Will her neighbors dislike her if she exercises her sexual freedom? Is it illegal? Will a police officer arrest her and a judge sentence her to prison? Fundamentally, does her desire for sexual freedom conflict with her desire to participate in her social community and stay out of prison? Again, to simply deny one's demonstrable social and legal context just because one wants to do something is profoundly irrational.
Finally, she will look at "theological" reasons. Does God prohibit her from exercising her sexual freedom? But theological reasons are substantively different from the preceding natural, secular reasons. It is true of reality that some things we might want to do actually do hurt others. It is true of reality that some activities will earn the disapproval or ostracism of our neighbors. It is true of reality that the government uses real police and real prisons to suppress some activities. So when faced with only theological reasons, how can anyone object that she wants to determine if theological reasons are also true of reality. And if they are not, she is justified in dismissing them.
Schumacher is essentially engaging in "underpants" reasoning. Although atheists disbelieve the existence of God for many reasons, and sexual morality seems pretty low on the list (based on my own informal knowledge of hundreds, perhaps thousands, of atheists), some atheists such as Huxley perhaps are motivated by escaping Christian sexual morality. But what of it? It is a post hoc ergo propter hoc fallacy to conclude that because Huxley desires to escape Christian sexual morality, and because Huxley is an atheist (or a believer in meaninglessness), he is an atheist just because of his desire to escape Christian sexual morality. And it is not a fallacy but an outright lie to claim without compelling, direct evidence that he has irrationally chosen atheism.
I suspect that many "fundamentalist" Christians (and perhaps Muslims) would decisively reject my central assumption, that wanting to do something, absent compelling reasons to the contrary, is sufficient justification for actually doing it. I suspect that for these "fundamentalists", wanting to do something actually raises a red flag, that wanting to do something compels deep moral scrutiny, that wanting to do something requires a positive, extrinsic justification. I also suspect that if a fundamentalist wants to do something he is extrinsically commanded to do, he will do it in a way he doesn't want to do it, just to avoid the appearance of "selfishness". If so, I would consider this attitude profoundly neurotic. I suspect that those such as Schumacher who make this kind of moral argument are simply demanding that the rest of the world share their neuroses.