And as far as I know, the hate does come from Nyssa's manipulations (repeated killing/Lazarus Pit resurrection), so it can theoretically be overcome. Right now she's not a fan of Bruce's, but I think she put the needs of Damian first, which is why she handed him over in the first place. Bruce could teach him things that she would not be able to, and she undoubtedly believed that the boy needs a father, even if it's Bruce.