Balance To The Force?
Balance isn't about killing the bad elements of something...
If anything eliminating all the evil brings about imbalance.
Balance is about an equilibrium between good and evil...neither one is above or has more power than the other.
The only reason why Vader killing the Emporer brought balance back to the Force is because the only remnants was Luke.
Basically put, if the pendulum swings in favor of one side, it has to swing back in favor of the other for balance to be maintained.
In a sense the prophecy may have talked about the one who would bring balance back to the force, but also the extinction of Jedi and Sith.