My reading is they were simply trying to comply with regulations. It wasn't about what ideas they believed the religious texts were trying to convey, but whether their content met a certain definition set by law. The law could be poorly written, or it could be poorly and over-cautiously interpreted by F-Droid maintainers. But I didn't get the feeling they were acting on any kind of moral judgement or own belief about what's appropriate for children.

Does the Bible encourage violence or promiscuity? Not really, no. Does it mention and describe those things in some detail? Yes, absolutely. If that's the kind of content you need to remove from your store, then obviously you need to remove the Bible from your store. Whether that was really the case seems questionable at best, but the stated logic seemed pretty coherent to me.