This is something I'm currently thinking about a lot, so you might want to ask me again in a few months.  But sections 4 and 5 of this essay on pragmatism by Roberto Unger, my favorite thinker, contains some choice quotations.  Unger bemoans "the overwhelming influence that the disciplinary structure of the modern university, with its obsessive focus on the filtering out of unreliable people and ideas, has had upon the way we do science."  But, as with most of Unger's work, you'll have to find the details elsewhere.

That essay, incidentally, is where I got the idea that the realism vs. constructivism debate is a pretty lie, covering up deeper, more unsettling concerns about how mathematics is actually practiced.  Unger calls it a way of "keeping disagreement within the family", and notes that it is by no means confined to mathematics.

Related to the project of restructuring the social organization of the university system is the project of reorganizing the language surrounding science.  Bruno Latour's excellent book Politics of Nature attempts to do just that, though I've just barely begun reading it.