Isn't there a way to drop your Dark/Light side points too? So you can play the story however you like and use whatever tool it was to remove/reset those points. It was like a year ago when this was discussed and since they wiped the old forums... so it could be removed or not implemented yet.
You can pick up Diplomacy as a crew skill and these missions will give you light/dark points but i would think it would be a grind.
or you can just keep doing flash points and just make the desired light/dark choices