What I was talking about was strong forms of methodological naturalism, the kind of MN that is supported by Hume's essay on miracles. You need a strong form of methodological naturalism to rule out ID in principle.
Lewis's book on miracles has the AFR in chapter 3, but it actually is there to set the table for reading the NT open to the possibility that there are real supernatural interventions. It is a case against the kind of MN we find in Bultmann.
I think MN needs some unpacking here. Obviously Jim, your understanding of MN is open to the possibility of discovering at the end of the day that there is evidence of design (even though, contingently, the evidence goes the other way). That's not what this passage is complaining about.
Just so you know, I would not have supported the Dover school board in its school curriculum decision. Nor would I have supported the silly sticker in (I think, Georgia). I would not have made the far-reaching statement that Judge Jones made, and I certainly would have been a pretty skeptical of the Barbara Forrest-style arguments that the judge accepted. I think even the Discovery Institute thinks the old Dover school board overreached. Evolution is the predominant paradigm in biology and ID simply has not, at this point in time, done the kind of science necessary to be going to public schools and saying there is anything more than a minority report that stands against it.