Thank you for your question. Due to the high volume of questions Dr. Craig receives, he cannot answer every one personally, although he reads each one. I am one of a team of volunteers that helps respond to Dr. Craig’s questions in a timely manner.
Dr. Craig is explaining what Western intellectuals generally believe—that the pursuit of reason will lead them to atheism. Of course, as Christians, we do not believe that.
So unless Craig comes out and says, “No, I was speaking for myself when I said ‘The person who follows the pursuit of reason unflinchingly toward its end will be atheistic or, at best, agnostic,’” I won’t be using that quote in the future. Though it wasn’t as obvious as Tom suggests that that wasn’t Craig’s position.
Normally, yes, I’d assume that a Christian isn’t going to think reason leads to atheism. Craig, though, has said he’d keep believing in the resurrection even if he went back in time and personally witnessed that Jesus’ body stayed in the tomb for weeks after Easter. That alone is enough to make you wonder. (Other telling quotes can be found in this thread, where I had originally found the “follows the pursuit of reason” quote.)