If you hurt a child I want to know your name
It is always desirable that a law which is penal in nature applies to the future not to the past. No person can be found guilty of an offence which was not considered so at the time of the act. That is a basic tenet of criminal law. However, the law the Fondazzjoni is objecting to is not directly intended to penalise pedophiles. On the contrary, it is meant to protect the victims of such crimes. It is intended to protect minors by preventing their becoming victims of known predators. The minors are the primary focus of the law and not the offenders.
The Fondazzjoni's position is unsound in that it would defy the scope of the law. Yes, sexual predators convicted prior to the coming into force of the new law should be registered. Being so registered is not a punishment for a crime committed prior to the enactment of the law. It is merely an administrative consequence of being so convicted. In practice, it is a measure that would make it that little bit more unlikely that a predator reoffends. And that, to my mind, is a good thing.