favoring his boss's boss (i.e. the university as a whole) instead of his boss (the math department)

Favoring the "goals" of the organization as an abstraction over the actual punishment/reward structure of the living, breathing, and interacting cogs of the organization.

I've come to look at bureaucracies as parasites on the host organization.

Aligning the goals of the bureaucracy with the goals of the org is actually a very hard, very interesting, and very important problem.