I've read a few of the essays in the book, including the Chomsky one, which has as little relation to the rest of what I read in the book as your own discussion does. Now, clearly the discussion has broadened here to questions of philosophy of science, and the nature of social science, and obviously I don't want to tell anyone to stop talking about that.
But I think it is worth emphasizing that there are a number of uses of "theory" to which these debates are not particularly relevant; your mention of political theory in this context seemed to be obscuring that point. I want to emphasize this point in part because of something Chomsky strongly suggests in his contribution to "Theory's Empire" (I'm not attributing this position to you): that the only form of thought or knowledge that isn't immediately and universally accessible is theory-construction in the specifically scientific sense; that something is either real science, or pseudo-science, or common sense. The disciplines that get lumped together as "theory" (political theory, literary theory, some sorts of social, anthropological and legal theory) are counter-examples to Chomsky's position.