IN his last major speech before leaving office, Dwight D. Eisenhower uttered his famous warning against the dangers arising from a mushrooming government bureaucracy.  His graphic description of a vast “military-industrial complex” won a permanent place among the catchwords that characterize our society. But who among us still recalls the concern he voiced over the threat of big government to higher education?  These words struck no spark in an era when universities could enjoy the fruits of Washington’s largesse with few restrictions or controls. Yet today, the President’s fears seem prophetic. In little more than a decade, relations between Washington and the academy have been transformed. After existing for generations as cloistered enclaves-free of even such basic requirements as workmen’s compensation and unemployment insurance-universities must now comply with detailed rules that cover a long and growing list of campus activities.