Well, it turns out that he was really warning about the “military-industrial-congressional” complex.
42-year CIA veteran Milton Goodman explains:
In the spring of 1961, I was part of a small group of undergraduates who met with the president’s brother, Milton Eisenhower, who was then president of Johns Hopkins University. Milton Eisenhower and a Johns Hopkins professor of political science, Malcolm Moos, played major roles in the drafting and editing of the farewell speech of January 1961.
The actual drafter of the speech, Ralph E. Williams, relied on guidance from Professor Moos. Milton Eisenhower explained that one of the drafts of the speech referred to the “military-industrial-Congressional complex” and said that the president himself inserted the reference to the role of the Congress, an element that did not appear in the delivery of the farewell address.
When the president’s brother asked about the dropped reference to Congress, the president replied: “It was more than enough to take on the military and private industry. I couldn’t take on the Congress as well.”
And see this:
Indeed, Congress members – part of the fatcat club which makes money hand over fist from war – are heavily invested in the war industry, and routinely trade on inside information … perhaps even including planned military actions.