Without expanding too much on the Legends content (I still love the term Expanded Universe), the Dark Side and the Light Side are integral aspects of the Star Wars universe, neither side stronger nor better. It's how it always was and how it always will be, for dark and light are just aspects of everything in life.
The Force, in the end, is merely energy, energy that is able to be harnessed by one for good or for ill.
Now, as it was expounded upon by others in this thread, the Sith are other users of the Dark Side are a different story. They use the Force for their purposes, be it for power, greed, fear, anger, etc. They corrupt others and the balance that is set in the universe tips to one side, which is why the Jedi are there to stop them, to extinguish them.
This is, as I see it, is why the Jedi know they can destroy the Dark Side. Not the dark aspects of the universe, for that will always be there, but the Dark Side that those use for their own reasons, that breaks the balance.