It's really the inverse of what you said. All equipment installed on an aircraft in compliance with the Airworthiness Standards and the Operating Rules must be operative. However, the Rules also permit the publication of a Minimum Equipment List (MEL) where compliance with certain equipment requirements is not necessary in the interests of safety under all operating conditions.
The removed A340 wingtip would be covered under the CDL (Configuration Deviation List). The CDL is not intended for use with damaged components. Damaged components may be replaced or repaired in with the Structural Repair Manual. If time does not permit replacement, permanent or temporary repair, or if the part is not in stock, then the component may be deferred against the CDL. Damaged parts may only be deferred against the CDL by removing the component, if it is listed in the CDL, and taking appropriate CDL weight and fuel penalties.
From reading the article there is no reason to believe that proper repairs were not made to the A340. The left 24 hours late with sheet metal repairs made, and the damaged wingtip removed, with performance penalties applied.