We arrived in Germany without visa just with marriage certificate and the germans dont even blink an eyelid!
It's the french and the greeks that didnt initially understand the regulations (as set out in eu 38/2004) but with D visa she should have 0 problems entering Germany! keep her calm and let her enjoy her time in Europe.
Also call ba to cancel the avios ticket within 24 hours of booking and you get everything back!