It's a very well done series of quests, it made me feel sick to my stomach. I knew that the tree spirit was also evil, and knew that it would breed destruction of some sort, but at the same time, it's obvious that the Crones are pretty terrible and nothing good would happen to the children (especially when you learn from Ciri's perspective that one the reasons the 'trail of treats' exists is to send off children that parents no longer want to/cannot look after).
Faced with the choice, I ended up saving the tree spirit and setting it free, hoping to put a dent in the Crones' power over the swamp. Not surprised that it extracted revenge against the village, but it kept its word and rescued the children - at least for now. The follow-up however, with Gran being blamed for their escape and getting cursed, and the consequence that the Baron dies, was pretty tragic. While he had made many terrible mistakes, I at least felt that he demonstrated a genuine remorse and was willing to try and make amends (in the Botchling quest). He also did right by Ciri too. As I said, a tragic end, but I'll stick with it - mostly because I can't stand to do anything to support the Crones, they are clearly twisted and were willing to give Ciri up to the Wild Hunt while also chomping on her for their own sick purposes. I do indeed hope we get the chance to do them in at a later point, and I anticipate it - doubt I've seen the last of them.