Problem with claiming that ganon contributed to this lies in the Sword of Six Sages he wields during the showdown with link he literally pulls the sword from his chest and slays a sage.
I like the idea though that the sword became focal point for dark energy.
Ganondorf doesn't go in for big chopping swords and it's too crude to be phantom ganon's, it's more akin to an executioners sword than anything, and note the seal on the sword is dispelled possibly indicating that akin to other supernatural beings it's strength finally superceded the seal (a la...