They weren't 'given a reprieve'. At the time of the race it was passed as legal during its inspections, if it wasn't then they would have had to modify it pre race, they passed it so it was legal full stop. If the rules are interpreted differently after the fact you can't penalize Red Bull for that. It's the FIA's fault not Red Bulls.
Now that the FIA have change their minds Red Bull are changing their design, what more can they do than that?