This is what I gather from Mortis:
- Son represents the nature of the Sith
- Daughter represents the nature of the Jedi
- Father represents the role of the Chosen One
- Son has long-lasting rivalry with the Daughter (Sith versus Jedi)
- When the Son attempts to kill the Father, he ends up hurting the Daughter instead; the daughter prevents this assassination attempt through self-sacrifice. (Jedi believe in self-sacrifice)
- The Father sets the stage for elimination of the Son afterwards through self-sacrifice. (Chosen One eliminates Sidious through self-sacrifice, restoring balance)
In the movies; balance was restored after elimination of Sith Lords or so the Jedi thought. The Mortis Episode is a reflection on Anakin's role as the Chosen One. Though the balance thing is admittedly confusing in its case.
I think that the Father's role of balance was similar to that of Revan; the latter Force-wielder managed to balance himself on the knife-edge of the philosophies behind both the dark side and the light side. Revan never hesitated to eliminate Sith Lords who schemed to destroy or conquer the Galaxy. However, Revan was also willing to work with those Sith Lords who were not a threat to the Galaxy. It is possible that Father's behaviour was a reflection on Revan. (Keeping in mind that Revan was regarded as a worthy candidate for this episode prior to its release)
Therefore, we can assume that balance can be restored through following ways:
1. By destroying the dangerous dark-siders
2. By ensuring peace between the light-siders and dark-siders in fair manner