Here is a summary (in English) about the grounds on which the lower court made the ruling, which I just quickly found:
First, the defence of “social adequacy” was did not exist and was therefore not available to justify certain actions which would otherwise be criminal (this appears to be a defence comparable to the rarely defence defence of “necessity” in English law). Rhe social adequacy of the religious practice of circumcision on children could not prevail over the “child’s right to self-determination”.
Secondly, the action of the Defendant could not be justified by the consent of the child, as he did not have the “intellectual maturity to give it”. Section 288 of the German Criminal Code requires that
Whosoever causes bodily harm with the consent of the victim shall be deemed to act lawfully unless the act violates public policy, the consent notwithstanding.
Thirdly, the court justified the decision with reference to Germany’s Basic Law - a constitutional statute similar but not the same as the European Convention on Human Rights. The court carried out a balancing exercise which will be familiar to anyone who has read a UK human rights judgment involving, for example, the right to privacy versus the right to free expression.
On the one hand, the court considered the fundamental rights of the parents under Article 4 (freedom of faith and conscience – very similar to Article 9 ECHR) and Article 6(2) (“The care and upbringing of children is the natural right of parents and a duty primarily incumbent upon them” – this has no direct equivalent in the ECHR but probably comes broadly under Article 8).
On the other, there were the rights of the child to “physical integrity” under Article 2(2). There is no direct equivalent in the ECHR, but Article 3 (which prohibits inhuman and degrading punishment) has sometimes been expressed by the courts in terms of the protection of physical integrity.
The court observed that there is an “inherent constitutional limit” to the religious rights of the parents, and that limit was breached by the religious circumcision. The court paid particular regard to the fact that circumcision led to the child’s body being “permanently and irreparably changed” and that it could affect his own religious interests later should he decide, for example, not to be a Muslim. The court also took into account the fact that circumcision would be a “visible sign” of the associated decision of the parents.
German court rules child’s religious circumcision can be a criminal offence – Analysis « UK Human Rights Blog