The way to get light side points you not only have to avoid killing civilians and choosing Dark Powers (which push you towards the Dark Side), but also have to save civilians that are being threatened by enemies. That is when you hear those villagers yelling help and Grans running up to punch or shoot them, you have to kill those enemies, and then you're supposed to get credit. If that isn't working, I don't know what will, sorry.
You could try "activating" (use key) the civilian after you save them I suppose. By the end of the game if you stay true to the Light Side your bar will be all the way into the Light and you'll get the bonus power, regardless.