Actually, you can! As long as you have one Independent character, your other two PCs can be wherever they want (Sith, Jedi, Republic, etc.) Cheerio!
Thanks, man. Also, you (or the admins) better change the FAQ! It says only one character in main factions...
Also, I have another question... Is it allowed to join two factions at once? For example, the GAR and being a Jedi?