Getting rid of the tree is not the same as killing Twilight off. What is Twilight Sparkle known for? She is very reasonable, studies hard, is a huge perfectionist, can go insane when things aren't right, is very geeky (etc etc). Tell me at what point does the tree effect her personality traits? The only thing it ever served as was a library, which there are plenty of in Equestria. And I don't really care about minor changes such as the tower.