It proofs Judge being right, thats the whole point here. Because of Judges actions, Sanji can achive greater things now. Oh man, isn't Judge such a great father?...
Helping his son becoming better, by modifying him when he wasn't born yet, as long as Sanji makes the best out of it, it's fine!
Sanji using it for good or whatever and it helping Sanji in doing it, makes Judges actions look less bad or even ''good''. You don't have a problem with that?