Yeah, headcanon is a funny thing. I once spoke with someone who thought that Sombra was a corrupted Starswirl T. Bearded. I actually had to point out to him that Sombra doesn't have a beard, you know, one of the defining characteristics of Starswirl!
Before, the Crystal Empire was twisted with malice and hatred; all of the ponies there were fighting over the wealth the empire contained. Then, a draconequus, similar to that of Discord but bearing a different title, cast a spell, removing all of the greed and hatred that the Empire held and putting it into the center crystal of the center city, which repelled the Empire's enemies. The draconequus ed the crystal into an amulet, burying it in one of the elder unicorn kings' tombs by feigning that it belonged to that king. He then fashioned the Crystal Heart and gave it to the Crystal Ponies to replace the center crystal. In exchange, he had each pony there swear an oath to be at peace, and that if they resumed their lives of hatred and selfishness, that a dark enemy would find the crystal of malice and use it to conquer them.
Later, the Crystal Ponies did break their oath, and fate demanded they be conquered. A young student of Celestia discovered the amulet, and, consumed in its power, he fled Canterlot in the darkness and went North, where he found the Crystal Empire and conquered it.
However, I do like your concept of Nefarious. It had parallels with J.R.R. Tolkien concept of Melkor, named Morgoth, who was the first enemy who was defeated, and Mairon, named Sauron, his servant, became the Dark Lord afterward.
I did not read any of those books but, If I recall correctly, I believe Sombra was based a bit on Sauron. I believe the amulet could potentially be the "Ring of Power." It does corrupt whoever wears it, very much like the ring does.