Vader brings balance to the Force by completely wrecking everything about it. Jedi are slaughtered, the flawed old codes forgotten, the Sith Lord is killed, and only one Jedi is left to start from scratch, with the lessons of the upheaval to share with his students.
The Jedi of the Old Republic were too strict and more about protocol than the Force. Qui-Gon will be back in some form in Episode III to reveal his new knowledge of the "living Force" to Yoda. The other Jedi were looking at the Force as carved in stone, not something that could change, "always in motion."
As far as Palpatine putting Anakin on the Jedi Council, it was just so he'd have a mole. He knew they'd deny him the rank of Master, something that would naturally set someone with Anakin's sense of entitlement in a more vulnerable position to be swayed towards the dark side.