(Updated to correct an error)
Kurt Keefner misrepresents Sam Harris, misunderstands his arguments, and fails to respond to the real arguments. He even misrepresents philosophies such as reductionism that would have taken 5 minutes of research on wikipedia to understand (he thinks that because "matter must be capable of more than what individual atoms and neurons are, [then] reductionism is invalidated." Wow.)
The entire first half of the essay is wasted on the misunderstanding that Sam Harris's arguments depend on separating our consciousness from our unconscious brain, and that choices come from our unconscious brain, therefore we don't make choices. In fact Harris's argument does not depend on this separation, because he's not arguing that we don't make choices.
The main point is that Kurt Keefner seems to think that we're all arguing about whether humans have the ability to make choices. We're not. Everyone acknowledges that we all have the ability to make choices based on deliberation. The question is whether the choice is the ultimate explanation for our actions, or the proximate explanation that can be ultimately explained by reference to our history, our genetics, or our environment.
Kurt Keefner thinks that "our basic decision to explore the world cannot be explained with reference to anything but itself," and is the source of our free will. I think the extent to which we choose to "explore the world," like all of our choices, is just a proximate explanation, not an ultimate one. He thinks that Sam Harris's requirements for a choice to be considered "free" are unrealistic. But that was the very point that Sam Harris was making: that free will, as a concept, doesn't really make sense. Mr. Keefner can argue until he's blue in the face that we have the ability to make choices, but he never actually responds to the basic arguments put forward by Sam Harris, making this paper both boring and a waste of time.