In the end I did decide to include some papers by neoclassical economists because they have done most of the important economic history data analysis of the last 40 years. For example, a well-known argument by Chandler states that the mid to late 19th century industrial structure is characterized by firms of increased "scale and scope". While it is a compelling argument (which is why we do read him), work by Jeremy Atack and others has dug into the manufacturing censuses of this time period and computed Gini coefficients for firm size and other statistics to see the real presence and impact of large scale firms on markets and industrial structure. The empirical findings confirm Chandler in some aspects, but they also open new avenues for exciting research questions when the results do not confirm his theory.
So, in general I found that if a particular unit was getting heavy on the social history and was making arguments that could (in theory) be empirically verified, I would bring in a neoclassical paper addressing the issue, and then either criticize the paper directly for not addressing the social history thesis or show how it has some good points. For example, while I do think the Chandlerian argument above is a good example of a thesis that can be at least partly addressed by some simple statistics of market concentration and firm size, some other attempts at dispelling a heterodox/radical theory of its validity largely miss the point: Rothenberg's work at constructing evidence of an integrated Northeastern market economy by the early 19th century is one example of this. She wants to disprove the moral economy arguments of some leftist and radical historians of the New England economy, but her data do not entirely support this thesis, nor do her conclusions follow from the results. (I wouldn't agree that the presence of integrated markets implies that New England farmers were inherently capitalist or market-oriented.)
Other highlights of the reading list: classics such as a short piece by Gordon Wood on the American Revolution, Fogel and Engerman's Time on the Cross, Sean Wilentz and the history of labor radicalism, a week of Kindleberger's The World in Depression, and W. E. B. DuBois' Black Reconstruction.
You can find the full syllabus uploaded to the course website here later today.