Apparently "weekends" in Bioware land last from Friday to Monday, so I was able to still play a bit of SWTOR last night. That enabled me to play my Sith Inquisitor through the Black Talon flashpoint I already did with my Sith Warrior. And just for fun and giggles I chose the "light side" option in my dialogue with the captain. And actually won the "roll", thus the group didn't kill the captain. And I was positively impressed how this did not only change the "fluff" of the mission, like the conversations. But it actually changed some combat sequences as well, at least for the trash mobs.
Only downside: Getting 100 light side points not only means you don't get 100 dark side points, but you actually cancel out 100 dark side points you earned earlier. Thus playing through the same flashpoint twice choosing different sides effectively nets you zero dark/light side points. And you'd need to either win the roll or have somebody else who choose the same option as you to win the roll to actually play through the different version. You might be better off replaying it choosing always the same side, but hoping that somebody of the other side wins to see the other version.