Yeah like I did. I just left the tree be. When I walked out and Saheila was like you gotta kill it for me, I was like, naahhh. I just ignored her.
Lorewise, Sebille dislikes the Mother. She has no qualms about killing her/it. Killing the tree makes the whole area hostile, true, but it's not like Sebille ever was some sort of role model among the elves. I found it kinda fitting with the whole "rogue/outcast" image. She has always been the kin-slayer anyway.
But I decided to leave the tree alone cause I needed all the merchants. Item-hunting every level and all that.