That could definitely be an issue. Balancing dynamic systems is hard, especially when you bring an entire new section online and connect it with the existing structure.
The EVE universe is imbalanced by nature and by design, but hopefully Dust's mechanics will make the actual gaming experience for Dust mercs fun nonetheless. I'd expect an equilibrium to eventually emerge where warring parties employ mercs of matched number, armament and skill, and no one can gain an upper hand. That's what tends to happen in EVE anyway -- the starmap reaches an equilibrium of victors and losers, and borders are quiet for some time until a large disruptive event occurs, upon which alliances go to war, conquer or collapse, and the starmap changes and resettles again. So I'm hopeful that the micro-experience will still be fun during these transitions, even if the odds are clearly against one side.