Perhaps there should be a "whitelist" of Freelancers and Mercenaries that we will allow to participate. Members of this whitelist could be chosen any number of ways, but they should have to prove themselves to the respective faction. Caelum's Freelancer "Shamayim" comes to mind.
Of course I am against non-faction members being used to disrupt the balance of the battle, but if one faction is lacking numbers, I think digging into the "whitelist" is acceptable. As for a limit system, we could impose a ratio of official members to hired hands. How do people feel about 3:1?