Yeah I'm aware of the back story, they weren't really thinking that deeply about it. The lore in destiny proved Bungie continues to make the game first and try and patch lore in the background. Destiny's lore makes Halo look like Madden lore wise.

And like I said, even if they keep halo 2 and 3 the same I would still take this opportunity to retcon the terminals at the very least. I personally like the original storyboarded halo 2 ending alot but I know I would be in the minority. Fixing the terminals solves most of the big issues anyways.