My Theory:
1.The Dark Council hears the news about the Emporer being died and begin a Civil War with one another for total control. Darth Marr (the oldest member of on the Council) maintains order, but joins the front line again the Republic.
2. The Dark Council perfects a devise to harness the power of the sun, the same devise used in KOTORs Annihilation, (which is about the son of Bastila Shan tracking down a council member and passes the knowledge of the device the the Republic).
3. The Sith True Bloods don't get wiped out instead they become fall back into the dark ages and battle among themselves (because their is a Sith member on Palpatines high council if you haven't read the Crimson Empire about the surviving member of Palpatines guards. This indicates that the Sith Purebloods have indeed Survived but the Jedi and Republic Imprisoned the force sensitives and left the weaker ones on Korriban and the other Sith worlds. They are still alive in the Lost tribes of the Sith Which is set from the time of Naga Sadow to the New Republic.
4. The Voss ended up going into exile themselves like the Gree and remained Neutral through out the galaxy (similar to the Hutt Cartel.
5. Once the Sith Empire fell it went back to the repetition of the events prior the TOR where a Jedi would fall to the dark side and cause a war leading up to the events of the battle of Russan when Darth Bane brought in the Rule Of Two.
These are good possible outcomes that could have happened.