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.
In an Open Thread comment beriukay mentioned that he's reading C.S. Lewis' Mere Christianity. I've been reading it too, for interesting reasons.
In my case it so happened that I started discussing faith with a long-time online friend whose spiritual views I didn't yet know, and he turned out to be a Christian with a high regard for the Bible, who also has an interest in science. As our discussion turned to our readings on spirituality, I acknowledged (I think it was me) that I probably spent more time on books that reinforce my point of view than on books that challenge it, perhaps a case of confirmation bias. (I've been exposed to many poor arguments for Christianity, and dismissed them; but possibly that was largely a function of having started out with that bottom line already written and picking arguments I wouldn't have much trouble refuting.)
In the spirit of experiment we agreed to a "trade" - he would read (thoughtfully and with an open mind) a book of my choosing on reasons to doubt faith, and I'd do the same with a book he chose on Christianity.
So the idea here is to pick a book that's the "best argument from the other side" (as in quote 3 here).
I recommended The God Delusion - I'm not sure if that's the best choice given the above intent, but it's what came to mind on the spot.
Would you make a different choice? If so, what?