I don't think the author is suggesting Purdue should cease all classified research, but that the rules governing classified research should only apply to that r

I don't think the author is suggesting Purdue should cease all classified research, but that the rules governing classified research should only apply to that research, not all of the university. The question he poses is extremely interesting: are students at Purdue effectively banned from doing a thesis on the foreign policy implications of the Manning or Snowden leaks? That would be very black mark on their record.