Where did you see that he ever said it was bad?And that was pretty hypocritical of Eisenhower; given that he rode the “military-industrial complex” to the Presidency.
Once he could derive no further benefit from it, he had to tell everyone how bad it was.
He simply recognized the power it held and didn't want it to get too out of balance.
The military-industrial complex was a huge buzzword back then and got a LOT of attention in media, song, etc.