The shuttle crew WAS part of the military while the military payloads were being deployed; they'd have been breaking quite a few laws if they weren't. That is, incidentally, one of the reasons why NASA has always kept a stock of inactive (not retired, not discharged) military personnel as part of its astronaut program: for legal reasons shuttle's military missions required the reactivation of the crew for the duration of the flight. OTOH, it could just as easily be true that Starfleet takes part in combat on behalf of the Federation military without actually becoming part of it. That would put Scotty's comment into an interesting sort of perspective. Picture that same conversation taking place on the ISS with a pack of orbital bombardment missiles being offloaded from a cargo ship. "This is clearly a military mission. Is that what we are now? Because last time I checked, we were scientists." That is, in fact, the entire premise of the movie. Marcus was envisioning a MILITARIZED Starfleet, one in which ships like the Vengeance would be the norm rather than the exception. It would be a massive paradigm shift away from everything Starfleet had ever been, away from all of its previous priorities, all its existence principles and values. What's also telling is that Marcus only could have made that transformation happen in the event of a massive and devastating war with the Klingon Empire. Marcus himself believed that Starfleet wasn't a proper military, and was willing to do some rather crazy things in order to change that. If Starfleet was ALREADY a fully prepared combat force, then the construction of the Vengeance and the destruction of the Enterprise is impossible to justify. Even more interesting is that Khan doesn't seem to think so either, since he mentions Marcus' "dream of a militarized Starfleet." Think what you will about Picard's moral pretenses, but I'm sure that Khan of all people knows a military when he sees one.