I think it's just there because it sounds pretty. Maybe the same voice that was used for Malon was used for the song? Idk. Regardless, I don't think it's a reference. Seems too subtle and takes too much inferring to be a reference for me.
Now call me crazy, but I read somewhere, a while back when the game had only been out for a year, that in the Japanese version there were a few references that prove that voice in the field at night in Twilight Princess was in fact Malon. It was about Giovani's quest, that the curse of gold had originated to his wealth which was from his ancestors that had often done bad things to acquire wealth during a time of conflict in the past. Talking to more NPCs some more and you find out that in the past a building in the middle of Hyrule field had been burnt down during a conflict from nobles of Hyrule.
Now I don't know if this is true or not, but I racked my brain and put two and two together and figured that should this information be true then...the building that burnt down was Lon Lon Rance and Malon was singing a song of sorrow for her destroyed ranch and that possibly Giovani's family and his curse was related to this incident. Nice huh? But if anyone can confirm this that would be great.