When I started the mod in first place, I did so, because of a couple of interesting jedi abilities I was able to implement with the game engine. Not because I thought we need a 1000th line battle mod. I would be very disappointed, if players weren't allowed to play some jedi on sith battles for fun. This is called "Bear Force II" after all. Think about it.
Game modes like "hero" or "random" can allow a good jedi/clone ratio and will probably make the best gameplay, but this is really a decision to make by the server owner.
Regarding balancing classes, I think there's no way people will have fun to play a battle droid and have his whole team killed by a single jedi.