Should there be a detailed survey when you log onto open about what community goals you're interested in and what side you intend to take if you get involved? Otherwise you might end up in an instance where the player split was 24/4/4 between people on your side, people opposing you and people having nothing to do with it. That would be pretty unbalanced too...
No, that's a strawman argument. First, don't let the perfect be the enemy of the good: just because it is not practical to eliminate all imbalances does not mean the most glaring ones shouldn't be redressed where feasible.
Second, while the scenario you are describing is not balanced, every player is at least in the same universe and has the choice of which side to work for. Obviously in any given conflict one faction or another will have an advantage; this isn't about changing that. This is about ensuring that no game mode has a constant, systemic risk-reward advantage (as opposed to having a temporary, somewhat random advantage due to more players happening to support a given faction).
Third, such an egregious imbalance isn't as advantageous as it may seem, especially if we are talking about combat. Sure, the 24 players would dominate that instance and easily farm NPCs, but a lot of those players would be wasted as there wouldn't be enough targets to go around. Those 24 pilots would have a much larger effect if they split into 6 wings of 4, went into private groups, and dominated 6 separate instances.