Bringing "Balance" to the force didn't really have anything to do with mathematics.
Plus when Vader killed Palpatine/Sidious, he was no longer a Sith but a Jedi, so you could argue that the score was 2-0, in favor of the Jedi. Then he dies, and then you're left with 1-0. That's still unbalanced, mathematically speaking.
Bringing "balance" to the Force isn't about evening out the Light Side and the Dark Side. The Dark Side, specifically in the manner that the Sith practice, is chaotic and upsets the Force. By destroying Palpatine/Sidious and dying, he removed the Sith from--and this is a really poor word choice I'm about to make--the equation. With no Sith practitioners, the chaos is gone, balance is restored, and everything resets back to zero.