I went all light side on my IA, and with the exception of people in flash points getting pissed when I won rolls that caused a light side branch there were no issues.
I dont think it works like that. Even if you win the roll and picked a light side choice, they will still get their darkside points if they chose appropriately. All your rolling for is the cinematic in most cases (aside from choosing if someone lives or dies etc). I.e if you win the roll and say live you get light side points and the dude lives. But your teammates who all selected die but lost the roll still get darkside points. C/D?