The repercussions of the feds' attack on privacy reach far beyond the interrogation room when coupled with an ecosystem of cowardly, risk-averse institutions like universities, which themselves are under increasing federal scrutiny.
There's cowardice and there's weakness. Because of the reduced enrollment nationally and the successful attacks on grants, universities have to compete for students now and it will be more difficult to take stands, just as us software-touchers find it more difficult to take the kinds of stands we like to take as our positions on the job market become less ironclad. The strong do as they will and the weak do as they must, but that doesn't really prevent the weak from nursing grudges for later.