If you don't want the object, don't return it. That's the easiest solution here. I'm going to suggest to the Google Plugin for Eclipse team that they change the template to not return the deleted object by default.
If you do want the deleted object, I think you're running into JDO's lazy loading. Your property degree
is being loaded at serialization time. However, since the underlying datastore object is already deleted, it can't access it. You'll need to explicitly access the property before it gets deleted.