The thing about the will of the Force is that almost all we hear about it comes from the mouths of the Jedi, and because they're the 'good guys', it tends to be accepted as truth. What the Jedi say isn't necessarily true and what they say and what they do aren't necessarily the same thing either. There will always be darkness, because darkness partly defines light and allows light to exist. The Force going out of balance was an out-of-control skewing in favour of the dark. Yes, that was largely due to the actions of the Sith, but the environment in which they were able to act so effectively was created by many other people, including the Republic, and their agents, the Jedi.