McIlroy's critique is both astute on it's own yet perhaps not relevant in the context of what Knuth had been asked to do, namely present an example of literate programming. That's not to say the McIlroy's script can't have a literate form, only that it wouldn't serve as a good exemplar.

It all serves as a good reminder of how Knuth's work should be used & viewed: It shouldn't be taken as insight into how to manage and develop for software projects. It's more useful as teaching tools for how to think about solving problems. In my mind it's the difference between "pure" science and practical engineering, though I'm not sure that's a perfect analogy.

To try another analogy, it's like Knuth was asked to make a custom set of clothes. And McIlroy's critique seems like saying "Not everyone can afford custom made clothes, and the GAP produces perfectly serviceable clothes that are far more practical in most situations" It's correct, sure, but rather besides the point in the context of the original request.