"Balance to the Force" is about the balance of nature where everything is in peace and order without anything to disrupt the peace. The Sith throw the force off balance by creating wars and using the Dark Side for their pursuit for absolute power so it is the Chosen One's job to destroy the Sith so that the Force will be brought back into balance.
It's not about equal amounts of Jedi and Sith, it's about the Sith being a disease to the galaxy and Anakin is the cure.