After reading the German court document linked in the CNN article (not a lawyer), it appears charging customers extra for not taking a leg of their flight is actually legal in the eyes of the court. They also cite a decision of the highest ordinary court in Germany (BGH) to that effect. I find that quite worrying.

The lawsuit was only struck down because of a lack of transparency in the pricing, as the customer has no way to check the fare they will end up with if they skip a leg. So if they publish prices for skipped legs, it would be a-ok I guess.