The Cult is not a religious organization from the viewpoint of the German government, but a profit-seeking organization. As such, the government considers the methods used by SC to be evil and aimed to set elemental parts of the German constitution out of power. It´s understandable that they don´t want to support the SC, directly or indirectly.
Moreover, my recollection is that Germany's current position on the cult is that a number of rather high-ranking Scientologists were involved in some sort of real-estate scam in the 1990s. I forget the details, however.