Best way to solve this is to give us options to disable 1 or 2 factions before a game. I predict we'd see a lot of reb/empire only games online, and I just might start playing it online again!
There's nothing about the ZC that isn't overpowered. Their units are expensive which helps to balance GC a little, but in skirmish battles (which is all I ever play online, mostly space skirmish, because I don't want to sit through a GC) ZC is overpowered to the extreme. Give us an option to disable them and all will be well.