To get what the OP wants would not only call for an engine overhaul like Daedalus304 said, but in actuality it would require completely new and different game.
I've always looked at the universe of STO as "Prime.5" It's not the goody goody socialist utopia of the Prime Universe, but on the flip side it's not as all out evil as the Mirror Universe, it lies some where in between. If you look at it that way, it is a tad easier to swallow. EDIT: Although I wouldn't mind Cryptic…