Personally, I feel like Jen Taylor is too much of an asset to the series for 343i to simply excise her character from it entirely. Thats from a business standpoint.
From a fan standpoint, there were plenty of loose ends to help Cortana's continuity/resurrection. There have been references to Cortana's "disappearance" into Requiems mainframe prior to Chiefs interaction with the Librarian. The fact that the Librarians plan incorporated "(Chief), (Chiefs) combat skin, even (Chiefs) ancilla Cortana" indicates a greater design or plan that would help maintain that continuity. Even the Librarian herself made a backup copy of her own memory to ensure the success of this as-yet-unclear plan. Additionally, Cortana's fragmenting of her processing matrix to thwart the Didacts counter-intrusion measures during the finale is itself indicative of her potential survival ("most of me is down there" [read: the ruins of the Composer, or in the ferro-electric data pulse which decimated New Phoenix? Either scenario lends itself to some kind of later reclamation]) And lastly: the fact that of ALL PLACES, "New Phoenix" was where they chose to stage the closing sequence? Names and their metaphors/implications have always factored strongly into the Halo series, and I struggle to imagine that the choice of a city named for a magical creature that is resurrected/renewed in fire is simply a matter of coincidence.
