Germany is not America, so they do not have the same political or religious freedoms as we do, however, as a country with a deeply rooted dark history of not only racial prejudice, but political and governmental activism as well as influence on personal religious beliefs, they should learn from their history and leave people's religious ideological beliefs, practices, and concerns to themselves and their decisions.
No, I don't think the German government should be meddling in the affairs of religion. I believe that separation of church and state is the way to go. Mosques should be allowed to do their own thing, just as churches and synagogues and other houses of worship should. Keep the government out of religion.
Government should not tell a religious group how to run things. As long as there is not harm coming to anybody things that have to do with your spirituality should not be under government scrutiny. Places of worship can't tell the government how they should run and they should get the same respect shown in return.
What happens within the mosques should not be determined by the German government. If something that happens outside of the mosque, which affects the general population or if something done in the mosque is hurting a German citizen, then the government should be able to step in. There should be freedom of religion to a certain extent.