I have been picking whatever feels right in the moment. Most of the time it's lightside but there are times when the dark choice feels the most appropriate. The way I see it if the person doesn't need to die to accomplish my goals then I will let them live. If they tried to kill me and are begging for mercy or trying to con me into letting them live, they die.
I kinda model my character after the bounty hunter in Cowboy Beebop. It never hurts to have people owing you favors. I know, they likely wont come into play since the whole story is scripted but its cool to pretend that, since I let this smuggler/slicer/etc live, in the future they owe me a huge favor.