I've got a feeling you've missed the point.
It's not about not refitting, but it's this constant demand for battle here, battle there and this constant feeling people are trying to imitate Edward James Olmos when they shout "We are at War!"
And, to be blunt, that people seem to want to play the Federation without playing the Federation.
"We are the Federation. We have Starfleet, dedicated to peaceful exploration and defending our people...and where are those battleships, battledestroyers and carriers?!"
The point is that to Starfleet dedicated warships are useless outside a war.
Conflicts come and got, but exploration goes on.
Hence the only ship we ever saw in the prime universe that was dedicated to warfare was the Defiant and her purpose was to defend against an enemy (the Borg).
Your also right. I WISH that cryptic could've made the game with some alternate diplomacy/exploration missions. But as it was stated before, this is unfortunately a MMORPG where most people only want to fight an blow things up. And I believe that Cryptic has done well giving the people what they want without compromising the ideals of Starfleet TOO much.
I do think that allowing the retrofit of lower tier ships would be a step toward recovering this image. Instead of captains getting progressively more powerful ships at every rank, perhaps we could customize what types of abilities/powers we upgrade our ships with?