My personal theory is that Equestria was created through the interaction of two primordial forces, one representing Chaos (Change, Motion, etc.), the other being Harmony (Stasis, order, and so on).
I think that the tree of harmony was the physical embodiment of the latter, while discord came into existence as the representation of chaos. The tree was an inanimate relic and the elements had to be used proper, so discord had free reign for a while.