Caldari,
I don't know of any such mods, but I am not sure they would do what you want anyway. I think maybe the real problem isn't the power of the systems, but the all-or-nothing nature of combat... regardless of how powerful weapons and defenses are, combat continues until all ships on one side or the other are gone.
A refinement for a GC3 might be to have a chance of disengagement for both sides after each round, with the probability of each side attempting to disengage being deterimined by the relative strength of both sides, the skill of the crews, and what "orders" they have been given (a simple slider-type variable indicating tolerance for losses). This might be more realistic, since in space (unlike at sea), there really isn't a way to "corner" your opponents, they can (theoretically) just engage their hyperdrive and leave whenever they want to.
Until then, though, I don't think there's much we can do to fix the situation with mods. You certainly CAN mod defenses to be stronger, but that will just prolong combat. When combat gets too long, it goes into arbitrary "sudden death" mode, which is even less like what you want.

GP