It seems clear that the story was gutted, but the reason is why? Joe Staten left for unspecified reasons, the Grimore stuff is barely incorporated into the game, there is clearly an underlying lore and story than in its final presented form is impenetrable.
Was is an internal conflict as to what the story should be? Was is done in a misguided attempted to drive players to bungie.net? Was is related to future DLC?
Who knows, but Bungie are not amateurs. A story as bad as Destiny's is not just the work of people who don't know how to form narrative in-game. Something is amiss behind the scenes.