If you read the Destiny issue of Newsweek, it clearly states that the Hive are a race born inside the darkness. While the Fallen are a once noble race, corrupted by the darkness. The physical similarities are mute. Look at many races from Mass Effect, they had the same 3 fingered hands and 2 toed feet, yet shared no common ancestry. It is most likely just an evolutionary coincidence. The descriptions come strait from Bungie.