I guess what I am trying to say is this: Real life war doesn't have balance. Why should a game?
As military personnel, you should already know the answer:
It depends on the game.
EDIT: More accurately, it depends on the rules of the game.
War games, as exercised by most militaries, are meant to be accurate simulations of real-world warfare, both symmetric ('balanced') and asymmetric, conventional and unconventional.
Most consumer (public) games are not meant to be as accurate or realistic as war games because of the consumer demographics. Most paying customers (who are paying for entertainment, rather than life-or-death) would rather have a taste of simulated war while still being rewarded for participating. Whereas in real, the consequences for losing are far harsher.
So your question should really be, what is PVP in Star Trek Online meant to be: a war game simulator, or something else?