All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
Allah accepts the repentance of the one who sincerely repents regardless of how great his sin.
Allah Says (what means): {But indeed, I am the Perpetual Forgiver of whoever repents and believes and does righteousness and then continues in guidance.} [Quran 20:82]
Therefore, your repentance is accepted, Allah willing; you are not subject to pay any expiation; making a sincere repentance is enough.
On the other hand, it is not allowed to leave your child with his mother unless she repents from her bad faith. You should take your child in your custody. If the mother refuses your demand, then sue against her in a court to take the custody of the child.
Know that if she was Kafir at the time of marriage contract, then the marriage is null. However, only belonging to the given sect is not a sufficient evidence to consider her as Kafir (non-Muslim). Instead, she should consider any act, utterance, or belief in what takes her out of Islam, to be disbelief.
However, the ruling of being out of Islam is applied only when all the conditions are met and there is no legal excuse for that. If the matter is as mentioned; i.e., she was Kafir then, the marriage is null, but the child will belong to you since he was born through doubtful marriage.
Finally, if this woman repents from the bad faith and deeds that are contrary to Islam, then you can marry her. In this case, you should renew your marriage since the previous marriage is invalid.
Allah knows best.