I've been starting the think that the spiritual world is harmonious because the unitary Intellect orders it, but that the reason for discord in the material world is simply because all souls collectively order it, and they are not necessarily in agreement. In a sense, each soul gets a vote corresponding to its area of influence and power—the World Soul is mighty and everywhere, thus the "laws" of physics are relatively uniform; but in your local area, it's the struggling wills of each of the souls in the that area, many of which may not be "in tune" with the divine and anxious after lesser Goods, and so you get local discord or even chaos.

If that's so, it neatly ties together Empedocles' Love and Strife with Plotinus' cosmology.