Don't overthink it. If it were me I'd book and fly. The major issue would be if she were denied boarding. Once you hit Germany you should be fine.The rule for Germany states the following in Timatic. Your wife would be considered traveling back to the family's home country so I don't see an issue.:

- passengers in transit to their home country, if there is no other travel option. The purpose of travel and the entry requirements for the destination and transit countries must be proved.