I like realistic balancing too and I agree - I usually hate it when something that's supposed to be nearly invincible in a tv show is nerfed to be just a bit better than other things in its related game, but in this situation it seems they're so overpowered there's no way to defeat them, a couple of cubes will completely obliterate anything in their path while adding more to the fleet each system they clear, even the combined force of multiple players won't defeat a bunch of cubes and assimilated capitals.
I'm currently playing as borg vs 3 unfair AI's that are allied with each other and so far I've utterly destroyed anything they throw at me and my fleet now consists of roughly 20+ capital ships from the other races, a few tactical cubes, spheres and assimilater cubes, the fleet does so much damage that warping in on a fully upgraded station or opponents fleet insta-kills them.
I've assimilated so many enemies that my support is somewhere around -4000. If the borg aren't meant to be a race you play with seriously (online) then that's fine, I like that, but if the borg are intended to be a balanced race, currently they're so extremely overpowered that you basically win the second the first cube has been built.
If it's possible - an alternate version of the mod could be made that has tv show balance, while the other has game balance, but I fear that'd be too much work for so little gain, but I'm just throwing it out there, personally I love the borg being this OP since it really does feel just like the show, but on the other side, there are people who'd want to play a balanced version of them for online games.