I hadn't actually thought about negative damage or lobotomizer.
Negative would seem a little odd, but it does open up a new strategy of using anti-matter on it, although that would mean it's been out a great number of turns so probably unworkable in most matches. I'd probably go for it eventually dealing negative damage, therefore making it more risky to play and hence less usable in certain cases (strengthening the argument for it being the un-upgraded card).
You're also right on the names, if they're swapped they seem a little odd. How about "Dying tree" and "Vibrant tree"? Although personally, since the Elder Tree has the potential to do more damage than a dragon if you use armour on it, I'd keep that one as the upgraded card.