I think it would be nice if the light / dark alignment had a similar role as in the KotOR games, albeit toned down.
Light / dark alignement should perhaps affect your weapons / skills; the closer you are to light, the more effective your non-lethal skills (healing, CC, shield) are, the closer you are to dark, the more effective your damage skills are.
It couldn't be as big an impact as it had in KotOR, as that could introduce balance issues, but a minor tweak of say 0.5% increase in effectiveness per level, with an equivalent decrease in effectiveness in the non-favoured skills.
It would perhaps make people more mindful of their alignment in terms of the role they wanted to play on their AC.
I think this would work if you made it something like force sensitivity for light and price of power for dark. By that I mean that these would give you lower ability costs (light) and higher damage/heals (dark) but you would also mean you take more damage from force attacks (light) and have less HP (dark). This would prevent DPS/Heals from going too far down the line if they want to raid and give those who stay neutral a small defensive edge for their troubles.