If a girl did something really bad that could not be forgiven and the girl's step-dad told the girl's little sister that she couldn't see he sister any more, could he do that, not the little girl see her sister anymore?

Praise be to Allah, the Lord of the Worlds; and may His blessings and peace be upon our Prophet Muhammad and upon all his Family and Companions.

There is no sin that is beyond repentance, but every sin even Shirk also is erased by true repentance.

 Allah says: " And those who invoke not any other ilâh (god) along with Allah, nor kill such life as Allah has forbidden, except for just cause, nor commit illegal sexual intercourse and whoever does this shall receive the punishment. The torment will be doubled to him on the Day of Resurrection, and he will abide therein in disgrace; except those who repent and believe (in Islâmic Monotheism), and do righteous deeds, for those, Allah will change their sins into good deeds, and Allah is Oft-Forgiving, Most Merciful. (Al-Furqan 25:68-70)

As regard preventing the girl from visiting her sister, it depends on the benefits and harms that may result from cutting relations. If the purpose of preventing the sinful sister from visiting her sister is to isolate her bad company or influence, or to punish her in order to give up the sin then it is allowed. If there is no such benefit in her desertion, then it is not allowed.

Imam Al-Iraqi wrote in Al-Ahkam as for the Hadith that reads 'there should be no separation between Muslims for more than three days,' it means that what is done for worldly or personal matters. Imam Al-Nawawi said the Hadith is true for what is done without any legal reason, if the separation is done for legal reason such as the person is bad due to his/her innovations, dissoluteness, or to avoid the bad influence of others, then it is allowed. What is reported from the Prophet (Sallallahu Alaihi wa Sallam) that the deserted Kab Ibn Malik and his two companions and order to the Sahaba to desert them is interpreted in this way.

The same is true with what is narrated from our good ancestors.

Allah knows best.