He also wasn't exactly disparaging it. He said we need it, but we must not let it become too powerful or influential. The truth of that hasn't really changed.
"In the councils of government, we must guard against the acquisition of unwarranted influence, whether sought or unsought, by the military-industrial complex. The potential for the disastrous rise of misplaced power exists and will persist."
He absolutely disparaged it, in fact he considered it a fundamental threat to democracy.
"Military industrial complex" isn't about maintaining a large, dominant military. It's about industry becoming so entwined with the military that they start calling the shots, and military decisions begin to be made for the benefit of corporations rather than the nation.
I'm not sure that means what you think it means. Eisenhower wasn't being complementary when he coined that term.