I've only played the games and haven't read/watched/listened to any of the other stuff out there for the Halo universe except a brief review on rampancy and another on the Human-Forerunner war, so my knowledge of what exactly the technological limitations are in the Halo universe is limited to "no time travel" (which is based on the inference that if it were possible then someone would have gone back to kill the first flood spore ever made).
With that in mind, the Librarian has demonstrated a knack for planning and foresight rivaling that of the First Civilization from the Assassin's Creed universe (who were so accurate in their predictions that you could actually have a conversation with the recordings of themselves they left behind). The Librarian made specific mention to the fact that Cortana and Chief's pairing was preordained, so I don't think it's that much of a stretch to suggest that she knew most or all of the dangers they would face together and made preparations to keep them safe (which accounts for Chief's insane "luck"). She may have allowed Cortana to leave Requiem still rampant because her rampant personalities were what allowed her and Chief to stop the Didact, and then used some crazy forerunner tech to beam her to safety.
My prediction for the future is that Cortana will be quarantined by the Librarian on a forerunner facility that Chief visits and her rampancy will completely overcome her. Chief will have to fight through the facilities defenses to reach some core computer or something where a device given to him by Halsey is supposed to fix her or at least put her out of her misery. That won't work, but Chief going to such lengths to save her will cause something to click inside Cortana and her rampancy will progress all the way to metastability. Reunited, Chief and Cortana go on to save the universe and either go out in a blaze of glory or ride off into the sunset.
