Thought? Comment? Pointed-sticks?
1) The FJ tech manual is a fan production almost 30 years old. I don't see how it's even relevant anymore (to the extent that it ever was) considering everything that's come after it.
2) The standing definition of "military" is an organization primarily tasked with national defense and border security, particularly against military threats from other nations and/or non-governmental organizations. An organization for which this is a secondary or supplemental mission role would, in modern terms, be described as "paramilitary" or even simply "armed."
3) Despite what many have said time and time again, the practice of maintaining a standing permanent military is relatively recent innovation in human history, and the blanket term "the military" even moreso. Starfleet exists on a spectrum of militarism closer to that of a police department or a coast guard: hardly "civilian" but nowhere close to a specialized combat-ready force.
I've been saying for years now that the depiction of Starfleet throughout eleven (now twelve) films and 24 seasons of television have depicted Starfleet as either a highly versatile and well-armed exploration program or a laughably inept military. The recent theme of "Into Darkness" not only reflects this trend, it's a ringing endorsement for it as clearly Admiral Marcus feels the exact same way about Starfleet and goes through some rather elaborate steps to militarize it (in addition to the direct implication from John Harrison that Marcus recruited him in the first place because the old-style concept of standing militaries is so anachronistic that the Federation barely knows how to do it anymore). Much of what you would expect FROM a halfway competent military is absent from Star Trek's depiction of the fleet, which is easy enough to reconcile by accounting for the notion that Starfleet equipment, training and doctrine puts a FAR greater emphasis on the peaceful and scientific use of its technology than on its defensive/security roles. Moreover, the handful of starships we've seen that actually specialize in combat are in EVERY case depicted as both controversial and highly unusual.
Put simply: too much gets by Starfleet, too much is absent, too much is simply forgotten or let slide for it to actually BE a full-time combat organization. Much of what happens on Star Trek makes a lot more sense if you compare their combat proficiency less to naval officers and soldiers and more to, say, police officers. Federation worlds undoubtedly DO have highly competent and specialized military forces for defending themselves from invaders, but in the age of automated/orbital defense platforms and ground-based weapons that can smash whole starships out of the sky, I doubt any of those military organizations have ever operated their own starships. Most fighting probably takes place on the ground anyway, and what little fighting DOES happen in space can usually be handled by Starfleet.