Having watched the video and read the letters, here is my summary of how it got ugly:
In refuting the notion that the existence of religious scientists itself is evidence that science and religion are compatible, Hoyne uses the existence of Catholic pedophiles as an example of humans being able to hold incompatible beliefs in their heads. This was a strawman (Hoyne didn't use this argument), and a rather low blow; there are any number of non-humiliating examples that could have been used to make the same point.
Haught, was quite understandably offended by this, and didn't want the video published. If, say, the National Academy of Science had been caught systematically raping children and covering it up, I suspect Coyne would be just as offended if the scandal were needlessly mentioned by his opponent in a public, and supposedly good-natured academic debate.