That was almost certainly the intention. But with the right equipment and information,
anything can be hacked. Consider that we're hacking the code of organisms to make them do things we want them to do, and that certainly wasn't the behavior they evolved to / were created for (depending on your philosophy there

). Consider that your keyboard - not even the computer, but just the subprocessor in your keyboard - is more advanced than any processor used to in the space shuttles, FAR more advanced than the computers used to calculate the moonshot.
Airiam's machinery almost certainly had diagnostic connections - probably wireless. But even if they were not wireless, and even if they had no diagnostic connections at all, they still had to be able to communicate with the NON-computerized parts of her in order to be useful to her. And there's a point of access. And the future AI that took her over knew its target and had 600 years of tech advancement and knowledge of cybernetics. It would be like asking IBM's Watson to figure out a simple 1-to-1 character-replacement cipher, only probably even more so. Honestly, as a computer tech, myself, I'm half-jokingly thinking the hardest part might have been figuring out the proper approach to take if someone had failed to keep proper archives of the documentation on her augment equipment in the intervening years.