You're assuming an absolute and direct correlation between the Jedi and Sith and light and dark sides, respectively.
Jedi =/= Light Side
Sith =/= Dark Side
Lucas says Anakin fulfilled the prophecy by destroying the Sith. If the Sith were directly correlated to the dark side, then he eliminated the dark side, which isn't balance at all.
"The overriding philosophy in Episode I -- and in all the Star Wars movies, for that matter -- is the balance between good and evil."
- George Lucas, quoted by L. Bouzereau, Star Wars: The Making of Episode I, 1999
"The idea of positive and negative, that there are two sides to an entity, a push and a pull, a yin and a yang, and the struggle between the two sides are issues of nature that I wanted to include in the film."
- George Lucas, Star Wars: The Annotated Screenplays
"I wanted to have this mythological footing because I was basing the films on the idea that the Force has two sides, the good side, the evil side, and they both need to be there."
- George Lucas, LA Times, 2002
"The Force has two sides. It is not a malevolent or a benevolent thing."
- George Lucas, Times Magazine, 1980
The dark side exists naturally, but the Sith through their machinations unbalance the Force toward it. The Jedi don't unbalance the Force toward the light side because they're allied with the Force, not to any side of the Force. They're keen on balance, that's why they want the Chosen One to balance the Force. And that's why they want to follow the will of the Force.