I'm fairly libertarian in my views, but I do agree with the City of Berlin in requiring commercial licensing and insurance on Uber drivers, as a consumer protection issue. How Uber chooses to solve this is up to them. They could require commercial licensing for all driver applicants, and provide the insurance on a per-ride basis, if this is legal in Germany.
HOWEVER, while this problem is separate from the medallion issue that Uber has faced in the US, only time will tell how the German local and national government treats Uber and other ride-sharing services. AFAIK, there is no set limit on the amount of commercial licenses and insurances in the city of Berlin, which is unlike how the medallions work. Medallions are not in place to provide consumer safety, but to limit the availability of providers. And protecting profit margins.
If Uber solves the issues presented and starts working with commercially licensed and insured drivers, but keep getting into trouble with the government, then we can start suspecting foul play.
And I'm not saying the official taxi companies played no part in this, they probably were very eager to tip off the local government of this legal issue