germany is federated, and education is in the purview of each state. so every state in germany may have different rules. that too was done with the goal to prevent nationwide indoctrination. besides, you got what, 2 or at most 4 hours of that subject, and it obviously didn't work to indoctrinate you. i was sent to religion class too, expressly to learn about other religions because we are not christian. if you want real christian indoctrination then you need to go to a catholic school where christianity gets into every subject, and being in school is like being in a monastery. again, the point is to expose children to different viewpoints. being a primarily christian culture, having a class about christianity is only fair. although today i hope that in most regions the class is not limited to christianity but also covers other religions, as it did btw in the school i went to several decades ago. in 9th grade we had the choice between religion and ethics. i chose religion. and if it were up to me, i would make that mandatory, because religion is a big influence in our culture, and we need to learn about it. not teaching anything about religion would be like not teaching history.
the problem with alternative people is when they isolate themselves from the rest of society. people should have freedom to believe what they want, but they should not get the freedom to completely lock out outside influences. our society lives from the input of different cultures and viewpoints. if you are isolating yourself from everyone, that may be ok for you, as an adult, but it is not ok for your children. they should make their own choice on whether they want to follow you or not. and it's our responsibility as a society to offer those choices.
take the amish in the US for example. they have their own way, but they are not completely isolated. and as i understand it in youth at one point each youth gets to live one year outside and potentially make a choice. for german expectations that's probably not enough. we want full integration, so your different beliefs need to be strong enough that they can hold their own against the rest of society. if they aren't, and if you feel the need to protect your children from general society, then i would wager there is something wrong.
also from a parenting perspective, if your children don't want to follow you then you are doing parenting wrong. as the adage goes, it is pointless to raise your children in a certain way, they end up copying you anyways. meaning, if they don't copy you you must have messed up badly.