There are much better sources on the subject than Dwyer. I would take his new two-volume biography of Napoleon with a very large salt pill.
I would suggest that you cannot treat the Germany of 1800-1815 as a monolith, because it was not a state in itself, but a collection of independent states. Both Prussia and Austria wanted to dominate Germany, and Austria invaded Bavaria twice during the period (1805 and 1809). And the major German states in western Germany (Bavaria, Wurttemberg, Baden, and Hesse-Darmstadt) chose to ally themselves with France mainly because they didn’t want to be ingested by either Prussia and Austria. Saxony joined the Confederation after Jena after being forced allies of Prussia.
Who were the allied soldiers who ‘behaved so badly’ in Germany? Most of France’s allies during the period were the minor German states of the Confederation of the Rhine, and those states cannot be classed as being ‘occupied’ in the sense of a foreign power. They were allied to France by treaty as the Confederation of the Rhine.
The reasons for the ‘unraveling’ of the Confederation of the Rhine are much more than a desire to kick the French our of Germany. Wurttemberg, for example, stayed loyal until after Leipzig when they were called home by their king, as Wurttenberg was beginning to be overrun by the allies. Saxony was treated shamefully by the allies, and, with the exception of Bavaria, the allied German states were overrun and the ‘requirements’ of the allies for continuing the war against France in both men and supplies was greater than Napoleon had ever required of them.