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I always took the "balance" line to refer to the fact that Anakin/Vader effectively ended the line of the Sith and paved the way for the Jedi to be renewed. Of course, he had to kill almost every Jedi first, but what can you do?
Remember, in Episode II, Mace, I think, makes reference to the fact that the Jedi's powers are seemingly waning. By causing this dramatic upheaval in the Jedi order, Anakin/Vader allowed a new generation of Jedi to be created, free from the problems of the past.

A.K.A. Mongoose, for you HLP denizens