I do believe this may be something of a malevolent spirit (wonder what would give me that idea). However, aside from me stating obviousness, remember how Ganondorf said at the end of Wind Waker about how he coveted Hyrule's Wind because it didn't bring Death? It's been confirmed that he originally went after the Triforce to get relief from the death-wind for his people, but along the way, he fell from grace, and he started to desire the world. Maybe Ghirahim's master is the true antagonist of the Zelda series, possessing Ganondorf, and influencing him to take the Triforce as his own. Perhaps this guy's name begins with Ganon, or ends with -dorf. I've seen it before (DBZ, Yu-Gi-Oh!) where when two people combine to become a separate entity, their name is a mixture of the two (Goten + Trunks = Gotenks, Goku + Vegeta = Gogeta/Vegeto, Gaia the Fierce Knight + Curse of Dragon = Gaia the Dragon Champion). Perhaps his name is Ganon, and he is the real Ganon we've come to see in the earlier and some later games.
But that's just my theory.