John Sterman's thesis also considers equilibrium vs. disequilibrium issues. You can search for it at the same MIT dspace link.
Static general equilibrium models may be the most common approach in economics, but there are increasingly many dynamic general equilibrium models (like MIT's EPPA) that combine short run equilibrium with long run dynamics in a few processes, like capital investment. The macro literature, particularly the endogenous growth thread, tends towards intertemporal optimization models, which are really just equilibrium plus perfect foresight, so it's worth looking at. The hot approach on the fiscal side of macro these days seems to be dynamic stochastic general equilibrium models.
Also take a look at Frank Ackerman's "Still Dead After All These Years," which is a critique of general equilibrium. As I recall, it's primarily technical (e.g., GE models don't have unique solutions). Personally, I think there are also major practical problems. My nutshell critique is that the typical GE (a bunch of nested CES production functions, plus an algorithmic search for a vector of market-clearing prices) is somewhat useful for understanding things like the incidence of tax changes on various sectors in the short run, or the relative magnitude of direct vs indirect effects of some policy. However, as soon as you consider any policy that's bigger than marginal tinkering, particularly for normative policy design, you're in trouble. First, it's likely that the elasticities that define your model are all wrong, because a variety of perception and action delays, and feedbacks like endogenous technology, are neglected. Thus seeming short-run rigidity of the economy that is in reality due to a mix of behavior and "physics" of the production landscape is attributed entirely to the "physics" portion, which makes it seem impossible to change anything without reducing welfare. Second, if unmodeled delays and feedbacks are in fact prevalent, preferences are endogenous, and institutions make rules that distort local incentives, the whole premise of equilibrium is silly. It's quite likely that the economy is far from equilibrium, and that while pressures move it in the right direction, social and technological forces evolve the landscape faster than the visible market economy can really approach equilibrium.