I tend to think of it in this way:
Positive Energy is the power of Creation. It heals, it energizes. Because Good deities are beings of creation, they naturally favor Positive Energy, as do their clerics. The energy itself may not be Good, but using it often is.
Negative Energy is the power of Destruction. It kills, it negates. Because Evil deities are beings of destruction, they favor Negative Energy, as do their clerics. The energy itself is not evil, but using it often is.
The correlation is there, as I see it, but an inverse of the common assumption. Negative Energy isn't Evil. Rather, Evil creatures tend to use Negative Energy, because Negative Energy is more compatible with their nature. Likewise Positive Energy isn't Good. But Good creatures have a natural affinity for Positive Energy, which is part and parcel of those things Good creatures value (healing, creation, birth, protection.)