don't think that it would be so efficiant to completly split starfleet into military and civilian departments. The reason being that fielding "civilian" exploration vessels would probably just result in losing a lot of ships. Your explorers and out-of-inner-territory science vessels have to be able to fend for themselves.
Of course these ships need to defend themselves, but throwing ships equiped for exploration onto the front lines is idiotic, as the ship will never be as good as a pure warship. Thats the problem.
You could, I suppose, crank out a lot more pure military vessels like the defiant, but then you're losing out on a lot of exploring and discovering that you could be doing instead. And one successful first contact could add a whole system to the federation. Which means more ships and personell down the line.
As I said, keep producing armed explorers, while at the same time produce heavily armed warships under the direction of a different organisation.
Also note that at the moment the Rommies are sort of our allies.
Not really. They only allied woth the Feds and klingons because they thought the Dominion was about to invade. And if they ever find out they were tricked then say goodbye to that alliance.
At the least we could count on them to join the fight against the borg. And since they're kinda between earth and the borg, expect them to take the worst of it.
True, although I think everyone would take up arms against the borg.
"You've all been selected for this mission because you each have a special skill. Professor Hawking, John Leslie, Phil Neville, the Wu-Tang Clan, Usher, the Sugar Puffs Monster and Daniel Day-Lewis! Welcome to Operation MindFuck!"