Instead of polluting your model with MongoDB specific classes like MongoDBRef, you should be able to handle it via conventions. For example,
If I have a model class with a foreign key reference like the following:
public class Employee{
public object Id;
public object Manager_Id;
}

I can create a convention where "Manager" is the collection name and "Id" is the field to join on. When a save occurs, the driver can detect this convention and apply the $ref appropriately.