This is a pointless argument until everyone agrees on the definitions of "Corporation" versus "University." The article is careless on that point, and vague about what we should do if they are really the same. He highlights a few exceptional cases, which may be representative problems but are probably not.

In particular, he doesn't seem to have thought at all about the consequences of levying taxes on Universities. That seems to be the central injustice he's concerned about, but does he really think the money would be better off in government hands? He doesn't seem to have considered those implications.

Personally, I think there is a ton of value in the idea of a University, in spite of the possibility for corruption and definitely in spite of anyone's attempt to abstract away random differences until corporations and universities look the same in some meaningless description. The culture of any decent university campus encourages learning in a way that you almost never see at a large company. You might compare Harvard to Google, or Xerox PARC, but start comparing second tier colleges to second tier companies and companies don't even come close.