It was in Ghosts of Onyx that Halsey and a few Spartans got trapped in the shield world. But there's a sequel book coming out that explains what happens to them in there (and I would assume whether or not they ever get out). But if it's Cortana, when did she and Chief get found? Last we saw them they were floating in space somewhere between the remains of the Ark and Earth.
Like I mentioned, it's my opinion it's Cortana by listening to the voices. The voice doesn't sound as much like Halsey. But I could be wrong. My reasoning to believe that it's Cortana is as follows:
Like I mentioned before, after the events of Reach (looking to just the games and not the books) Halsey is never mentioned after Reach. Why would she give a synopsis of the covenant/human war and what occurs after Reach when no one know's where/who she is?
Cortana is somewhere in space with the chief at the end of Halo 3, we all know this, but that's not to say that the event's taken place after Reach weren't cataloged by Cortana between Halo 2 and 3. Remember, by Halo 3, part of the Covenant have joined forces with the humans to fight the Higher Archs and the "Great Journey." By the middle of Halo 3, Cortana is back with Chief on Earth for a short while. With the narrative describing the events of what happens between the human and covenant at the end of Reach, I believe it's Cortana.
Of course this whole discussion is over analyzing the entire ending of the game. It's always interesting to see/read other peoples perspectives on how they viewed the ending.
As far as the novels go...Yes, ultimately it's Bungie's baby and they can do whatever they want. However, that being said, The Fall of Reach was labeled as "The official prequel to the award-winning Xbox game!" In the acknowledgments Eric Nyland thanks Eric Trautmann for "providing background material, editing, reality checks." For those who don't know, Trautmann was one of the three originating writers for the Halo story. So, even though it's Bungie's baby, I can see how some fans may be a little dissapointed with the story and what their idea of the in-game story could have been. Myself, I loved it and I can see why Bungie changed it up a bit and I wasn't dissapointed.