After some experimenting, I may have figured out the "issue", although this is really still a bug. I went back a few saves to before turning in the Shadow Prince's heart. I ate the heart, which I actually meant to do originally and forgot to do. But upon eating the heart, when you talk to the Scion, and then go back outside to get the request to kill the tree from Sahilia, you then get a slightly different dialog with Sebille, although you still don't get a choice in what she says. She says something like, "I may consider this because she is corrupted." Before it was "I can't do this because I'm the new mother".
I also had her refuse to become the new mother, and the Scion goes hostile. But I just ran out with Sebille, Sahilia is there, but she asks, "Where are all of your friends?" so you have to bring the whole party out one at a time to start the "Kill the mother" dialog. Ugh...
Anyway, this really needs to be fixed, I'm not sure if I feel like going through the whole fight in the tree again...