Why 'should' have? The rule states the FA 'may' remove points from a club, not have to, and certainly it doesn't have to dock unwon points. Previous precedent has been to remove won points in which the player has played. For example the MK Dons were docked the 3 points they won when the unregistered player came on as a sub and scored the winning goal. In the 4 league games the Sunderland player played, they won a grand total of 1 point, and even then, were winning 1-0 before he came on as a sub. In the cup, they were getting beat, until he went off......
When the FA fined Sunderland, every owner\managing director of every club in the Premier League was informed of the discretion, and of the fine, and not one raised a complaint as we were effectively down barring a miracle. As soon as the miracle started taking shape, that's when they decided to complain about it.