What evidence do you have that Napoleon would have destroyed Bavaria, Wurttemberg, Baden and Hesse-Darmstadt? They were already allies, thanks to the aggressively expansionist policies of Austria and Prussia. And Saxony wasn't destroyed by Napoleon, but negotiated with to become an ally, something the Prussians never thought to do. And Napoleon did that after Saxony had taken up arms, albeit forced by the Prussians, against France?
Napoleon also formed the Duchy of Warsaw and the Kingdom of Italy as allied or client states.
And this was worse than being overrun and absorbed by Russia, Prussia, or Austria how?