it is naturally regarded as having a publicist agenda, that is, as intended simply to promote the book
Right off, I suppose I should say that I have not read that book of Coyne's -- and probably never will, the major reason being that
I am already persuaded that evolutionary theory is "true": it seems to me something of a golden key for biological understanding, providing an extraordinarily successful systematic scheme for unifying an enormous range of biological observations from the biochemical to the paleontological. On the other hand, though it is far outside of my expertise, I might sometime look through his book on
Speciation since the topic is interesting and important, and since I might expect detailed scientific ideas there
Next, I'll say that if I had ever heard of Haught, I had forgotten it -- so I had to look him up to try to learn about his views. It seems to me Haught understands completely why some people think "the Darwinian understanding of evolution has made the idea of God completely superfluous, and hence unbelievable" (as discussed in his
pdf conference prospectus). Haught's notion is that
... The conversation between science and religion has allowed us to be able to formulate more clearly than before just what science is all about, and just what theology is all about. Before we did that—for example, before Galileo—“truth” was often a homogeneous mixture of common sense, theology and church authority, and natural philosophy; it was a smudge. But after the conversation between science and religion got going, especially after Galileo, what happened eventually was that we got to see more clearly what science is about and what kind of information it gives us, what it leaves out, and so forth. And the same with theology. We came to realize, for example, that theology can no longer moonlight by giving us scientific information. One of the most important developments in modern religious history—people tend to forget about this—was expressed by a rather conservative Pope, Leo XIII. In his 1893 encyclical Providentissimus Deus he instructed Catholics not to look for scientific information in the Scriptures. The biblical scholar Raymond Brown once commented that this simple instruction spared several generations of Catholics some of the anguish that non-Catholics have experienced in trying to reconcile Genesis with modern science. Of course, Galileo himself had already said virtually the same thing ...print interviewYou can get a more extensive look at Haught's pov from this
video interviewBased on this, and on reading Coyne's comments in the OP, I would guess: that the points of dispute between Coyne and Haught are metaphysical, rather than scientific; that Haught correctly understands that such metaphysical disputes are outside the realm of science and cannot play any role in science; and that Coyne does not really understand much of what Haught says, so is reduced to accusing Haught of intellectual dishonesty. Of course, I do not think Coyne would be obliged to agree with Haught, if he actually understood what Haught was saying -- I just think there's no evidence Coyne understood what was being said