Is there a way to remove yourself from this?

Sure: There is a third box "no confession" next to "Catholic" and "Protestant" on the form. You can check that and those 9% remain with the state instead.

German secularism has a few more peculiarities. Many charitable organizations e.g. running hospitals or institutions caring for the homeless, elderly, and disabled are in fact religious (Diakonie, Johanniter, Caritas, Stadtmission, ...). This has some unfortunate effects: They often hire people of Christian faith only, meaning atheists or adherents of other religions are mostly excluded at these organizations. There have also been cases of a doctor at a Christian-run hospital denying the abortion because of their faith -- despite abortion being legal here. However, much of the money these organizations receive is in fact public money, supposedly spent on serving the public. Another wrinkle is that Religious Law is used when it comes to e.g. prosecuting rape cases involving priests etc. Somehow, this separate system of law that doesn't really seem to work particularly well is accepted by the German state.