Well, to my ears, for someone to say that Starfleet has to militarized it sounds wrong. Starfleet is already the military. For me, it's like going from zero to ten, when Starfleet is already a ten, so to speak.
Without a script of the film handy, I can't say for sure what Marcus wants. However, from what I have read in your reply, I am reminded of a situation that arose during the Cuban Missile Crisis. President Kennedy and Chief of Staff Curtis LeMay had differing views on how to resolve this crisis. The president was in favor of a blockade, and the chief of staff was in favor of bombing the missile sites. Curtis would later say the peaceful resolution of this crisis was the greatest defeat faced by our nation.