Prof. Witt made many good points. He talked about the distinction between "hypothesis", "law", "fact", and "theory". Although he didn't quote Stephen Jay Gould, I think it is fair to say that he agreed with Gould's definition of "fact" as "confirmed to such a degree that it would be perverse to withhold provisional assent". Prof. Witt pointed out that evolution is both a fact (in the sense that common descent is well-confirmed and organisms today are different from those in the past) and a theory (in the sense that we have explanatory mechanisms such as mutation, natural selection, and genetic drift, to name a few, that explain how evolution took place). He also did a good job in exploding the silliness that is Behe's "irreducible complexity".
Prof. Witt did get some minor details wrong (like the old name of the Discovery Institute's Center for the Renewal of Science and Culture, which is now simply called the Center for Science and Culture). I also had some quibbles about his assertions that religious claims are unfalsifiable. Clearly some religious claims have that character, like "faith alone saves". But when religions claim, for example, that intercessory prayer works, or that a wafer actually becomes the body of a person, or that a statue cries tears of real blood, these can be tested. Even claims about the afterlife, which might look unfalsifiable at first glance, can be addressed to some extent, based on our current understandings about the biological building blocks of living beings, and chemistry, and physics.
The most significant disagreement I have with Prof. Witt was during the question-and-answer period. A student told the story of a group of evangelists who, suffering hunger and poverty, prayed to the Christian god for food and dozens of fish jumped into the boat, enough to feed everyone. He asked, What did Prof. Witt make of this event? (It wasn't clear to me whether this was the Bible story or a claimed modern-day story.) Prof. Witt answered that "Correlation is not causation", which I think was a rather weak answer.
Here is how I would have answered. First, I strongly doubt that the claimed event took place. Reports of miracles are common, but experience tells us that upon closer examination, these "miracles" almost always were entirely made up, or were wildly exaggerated, or had prosaic explanations. Remember the miracle of the juniper bush?
Second, let's suppose the event really did take place as claimed. How uncommon was it? Heck if I know; maybe fish jump into boats all the time. One would have to estimate the probability of the event, and the number of people in boats who prayed for food.
Third, science doesn't do so well in explaining one-time anecdotes. If the claim is that prayer works, how can we test that? Well, there have been a number of tests of this claim for intercessory prayer, and the results are not too favorable to the hypothesis that prayer works.
If prayer did work in a more or less consistent basis (say, 1% of all prayers were answered), this would represent a currently-unaccountable regularity of the universe that we could study. How, exactly, does this answering work? What if you pray for X and I pray for not X? Does your probability of success increase if you pray more fervently, or more frequently, or if you get more people to pray at the same time? Or if you pray for reasonable things versus unreasonable things? All these can be tested.
Ultimately, I think Prof. Witt missed a teachable moment.