Lewis actually asserts that indeterministic naturalism admits something other than nature, not something supernatural, but rather subnatural, and therefore on his view indeterminism and the quantum-mechanical level is in conflict with naturalism.
What he says is:
Now it will be noticed that if this theory is true we have really admitted something other than Nature. If the movements of the individual units are events 'on their own', events which do not interlock with all other events, then these movements are not part of Nature. It would be, indeed, too great a shock to our habits to describe them as super-natural. I think we should have to call them sub-natural. But all our confidence that Nature has no doors, and no reality outside herself for doors to open on, would have disappeared. There is apparently something outside her, the Subnatural; it is indeed from this Subnatural that all events and all 'bodies' are, as it were, fed into her. And clearly if she thus has a back door opening on the Subnatural, it is quite on the cards that she may also have a front door opening on the Supernatural-and events might be fed into her at that door too.
So, contrary to what Jason says, I don't think Lewis is considering non-deterministic forms of naturalism in this chapter. What he's saying is "these guys aren't really naturalists, naturalists have to be determinists."
The real problem with using this against Lewis's argument is that when you look at what Lewis says is missing from a naturalistic understanding of reason, namely, the relevance of ground-consequent relations and the perception of ground-consequent relations in a world governed by blind cause and effect, you find that denying determinism doesn't get the naturalist where the naturalist wants to go in overcoming what Lewis takes to be the "cardinal difficulty."
One of the complaints that I am going to be making against Beversluis's discussions of Lewis is that he too often presents a problem for what Lewis says without determining whether this problem can be easily fixed by a Lewis-friendly philosopher. On the other hand, in this case Beversluis doesn't seem to me turning this into one of the primary objections to Lewis's argument.