"Good" or Neutral Route is accomplished by making Peace. Reyyoshi already descriped what you need to do.
However not every Peace Ending is ultimatly good in a way. It is even possible to make Peace with several People and NPCs being dead, becuase the option to make peace only hinges on finding the culprit.
In the following Link you are going to find two possible Endings for the "Good" Route, that imo are the best. The first one maximize the benefits for the Players and important Characters while keeping the Life Lost Count to a minimum (only the Spy dies). The second, I call it "Thane's No Casualty Route" allows you to make peace, while keeping everyone alive (Downside: Cold relation with nauxus).