My adivce is to not pick choices based on keeping neutral....
That would be like going to the captain who you can kill and start thinking I killed the last two npcs ... Then I should let you live even though you did something worse then the last npc I killed...
Choose based on what you belive your toon would do.
You can always do crew skill quests to try to keep neutral but in reality you will find your self leaning darkside or light side.
To me a neutral toon is one that ranges from low dark level 1 to low light level 1.