If by "high regard for the Bible" he means inerrancy, I recommend The Human Faces of God as a first step.

It covers disturbing passages that I believe damage the credibility of the Bible as a whole. Biblical genocide, slavery, propaganda, early Israelite polytheism, contradictions, and failed prophesies of Jesus are all discussed with footnotes to additional literature. Most of this material is "standard fare" among critical scholars - even the idea that Jesus was a failed prophet - but church-going people are still in the dark on most of these issues.

It might help that the author of this book is a professing Christian. Your friend will be more open to criticisms of the Bible coming from another person of faith. It will help him explore radically different versions of (liberal) Christianity, even as he considers atheism.