No, he just said it's not PURELY a military organization, which is pretty hard to debate if you look at TNG. They're obviously not just an outer space version of a military. If you acknowledge that their primary mission is exploration, how can you then say that they're purely military? What country has a military with a primary mission of scientific exploration???Yes, Starfleet has defense as part of their responsibilities, but no less an authority than the creator of Star Trek itself, Gene Roddenberry, didn't like the trend in TWOK and TUC of accentuating Starfleet's more militaristic traits.
In times of war, like the Dominion War, yes they're the ones called on, but they're not just a military.