And it is thoughtful, for sure, and smart, and interesting. But I think it concedes too much to really existing economics. In particular:
Obviously, macroeconomic phenomena are the aggregated (or, if you like, the emergent) consequences of microeconomic interactions.No, that isn't obvious at all. Two arguments.
First, for the moment, lets grant that macroeconomics, as a theory of aggregate behavior, needs some kind of micro foundations in a theory of individual behavior. Does it need specifically microeconomic foundations? I don't think so. Macroeconomics studies the dynamics of aggregate output and price level, distribution and growth. Microeconomics studies the the dynamics of allocation and the formation of relative prices. It's not at all clear -- it certainly shouldn't be assumed -- that the former are emergent phenomena of the latter. Of course, even if not, one could say that means we have the wrong microeconomics. (Shalizi sort of gestures in that direction.) But if we're going to use the term microeconomics the way that it's used, then it's not at all obvious at all that, even modified and extended, it's the right microfoundation for macroeconomics. Even if valid in its own terms, it may not be studying the domains of individual behavior from which the important macro behavior is aggregated.
Second, more broadly, does macroeconomics need microfoundations at all? In other words,do we really know a priori that since macroeconomics is a theory of aggregate behavior, it must be a special case of a related but more general theory of individual behavior?
We're used to a model of science where simpler, more general, finer-scale sciences are aggregated up to progressively coarser, more particular and more contingent sciences. Physics -> chemistry -> geology; physics -> chemistry -> biology -> psychology. (I guess many people would put economics at the end of that second chain.) And this model certainly works well in many contexts. The higher-scale sciences deal with emergent phenomena and have their own particular techniques and domain-specific theories, but they are understood to be, at the end of the day, approximations to the dynamics of the more precise and universal theories microfounding them.
It's not an epistemological given, though, that domains of knowledge will always be nested in this logical way. It is perfectly possible, especially when we're talking societies of rational beings, for the regular to emerge from the contingent, rather than vice versa. I would argue, somewhat tentatively, that economics is, with law, the prime example of this -- in effect, a locally law-like system, i.e. one that can be studied scientifically within certain bounds but whose regularities become less lawlike rather than more lawlike as they are generalized.
Let me give a more concrete example: chess. Chess exhibits many lawlike regularities and has given rise to a substantial body of theory. Since this theory deals with the entire game, the board and all the pieces considered together, does it "obviously" follow that it must be founded in a microtheory of chess, studying the behavior of individual pieces or individual squares on the board? No, that's silly, no such microtheory is possible. Individual chess pieces, qua chess pieces, don't exist outside the context of the game. Chess theory does ultimately have microfoundations in the relevant branches of math. But if you want to want to understand the origins of the specific rules of chess as a game, there's no way to derive them from a disaggregated theory of individual chess pieces. Rather, you'd have to look at the historical process by which the game as a whole evolved into its current form. And unlike the case in the physical sciences, where we expect the emergent phenomena to have a greater share of contingent, particular elements than the underlying phenomenon (just ask anyone who's studied organic chemistry!) here the emergent phenomenon -- chess with its rules -- is much simpler and more regular than the more general phenomenon it's grounded in.
And that's how I think of macroeconomics. It's not an aggregating-up of a more general theory of "how people make choices," as you're told in your first undergrad economics class. It is, rather, a theory about the operation of capitalism. And while capitalism is lawlike in much of its operations, those laws don't arise out of some more general laws of individual behavior. Rather they arose historically, as a whole, through a concrete, contingent process. Microeconomics is as likely to arise from macroeconomics as the reverse. The profit-maximizing behavior of firms, for example, is not, as it's often presented, a mere aggregating-up of utility maximizing behavior of individuals.  Rather, firms are profit maximizers because of the process of accumulation, whereby the survival or growth of the firm in later periods depends on the profits of the firm in earlier periods. There's no analogous sociological basis for maximization by individuals.  Utility-maximizing individuals aren't the basis of profit-maximizing firms, they're their warped reflection in the imagination of economists. Profit maximization by capitalist firms, on the other hand, is a very powerful generalization, explaining endless features of the social landscape. And yet the funny thing is, when you try to look behind it, and ask how it's maintained, you find yourself moving toward more particular, historically specific explanations. Profit maximization is a local peak of lawlikeness.
Descend from the peak, and you're in treacherous territory. But I just don't think there's any way to fit (macro)economics into the mold of positivism. And there's some comfort in knowing that Keynes seems to have thought along similar lines. Economics, he wrote, is a "moral rather than a pseudo-natural science, a branch of logic, a way of thinking ... in terms of models joined to the art of choosing models which are relevant to the contemporary world." It's purpose is "not to provide a machine or method of blind manipulation, which will furnish an infallible answer, but to provide ourselves with an organized and orderly way of thinking about our particular problems." (Quoted in Carabelli and Cedrini.)
 Economist readers will know that most mainstream macro models, including the "saltwater" ones, don't include firms at all, but conduct the whole analysis in terms of utility-maximizing households.
 This point is strangely neglected, even by radicals. I heard someone offer recently, as a critique of a paper, that it assumed that employers behaved "rationally," in the sense of maximizing some objective function, while workers did not. But as a Marxist that's exactly what one should expect.
EDIT: Just to amplify one point a bit:
I suggest in the post that universal laws founded in historical contingency is characteristic of (some) social phenomena, whereas in natural science particular cases always arise from more general laws. But there seems to be one glaring exception. As far as we know, the initial condition of the universe is the mother of all historical contingencies, in the sense that many features of the universe (in particular, the arrow of time) depend on it beginning in its lowest entropy (least probable) state, a brute fact for which there is not (yet) any further explanation. So if we imagine a graph with the coarse-grainness of phenomena on the x-axis and the generality of the laws governing them on the y-axis, we would mostly see the smoothly descending curve implied by the idea of microfoundations. But we would see an anomalous spike out toward the coarse-grained end corresponding to economics, and another, somewhat smaller one corresponding to law (which, despite the adherents of legal realism, natural law, law and economics, etc., remains an ungrounded island of order). And we would see a huge dip at the fine-grained end corresponding to the boundary conditions of the universe.
FURTHER EDIT: Daniel Davies agrees, so this has got to be right.