Tomorrow is Yesterday
Christoper: I see. Did the Navy...
Kirk: We're a combined service, Captain.
Whom Gods Destroy
Garth: You, Captain, are second only to me as the finest military commander in the galaxy.
Kirk: That's very flattering. I am primarily an explorer now, Captain Garth.
Kirk: I agree there was a time when war was necessary, and you were our greatest warrior. (He is speaking to Garth.)
Star Trek II
Chekov: The order comes from Admiral James Kirk.
David: I knew it! I knew it! All along the military has wanted to get their han...
David:I've tried to tell you before. Scientists have always been pawns of the military---
Carol:Starfleet has kept the peace for a hundred years, I cannot and will not subscribe to your interpretation of this event.
You forgot the most important one:
Errand of Mercy
: I'm a soldier.
Pretty much sums it up right there. Roddenberry didn't start putting flowers in the phaser collimators until TNG.