I think you need to change how the Dark and Light side works, bellow I have listed some changes that could help the popularity of both factions and maybe help balance servers.
Evil Races Sith Warrior/Marauder Sith Sorc/Assassin
Good Races Jedi counter part
Neutral Races Bounty Hunter Troopers Agents and Smuglers
Neutral races would then choose light or dark side at the end of there quest chain around level 10. This would mean that the people that are playing set classes due to how they look or based on any other reason, would still have the option to play both sides which could cause a more balanced server. I only sugest this because on many servers republic and empire are unbalanced, and something as simple as this could allow players to switch sides.
as for how this would fit in with lore,
Bounty hunters work for money and who ever pays the highest so in all fairness they should be able to choose what side they fight for.
Troopers are the front line soldiers fighting the war and in this case both sides have them so why not.
Agents could be seen as double agents working for both sides.
Smuglers just like bounty hunters they are in it for the money.
One of the problems with this would mean do the good only get light side options and the evil get dark side?
No you could keep light and dark side options based on how you want to play your character but just have the initial quest that sets you on your path high lighted.
And for those that have already higher level there could be a one time quest that they could perform to choose there faction, this would allow players to switch sides and maybe balance the servers.
Failing any of these sugestions you could keep Evil and Good seperate and keep Neutral Neutral, and allow them to switch between the two factions to bolster which ever needs it just like many of the planets Republic and Empire fight over.
Feel free to leave feed back or indeed sugest other ideas to make this a stronger idea or flame the hell out of it either way do something.