Who's to say it didn't.But even if they render it neutered somehow, the only reason they'd have to trap it, as you say, is if they couldn't destroy the bad code that made it malevolent in the first place. And all that time lapsed may as well be an eternity for that bad code to resurface and replicate.
By the time Craft showed up, it could be hiding inside of Zora.
Craft obviously wasn't going to be the one to help the AI get free from it's cage.
Unless it hid part of itself in the Shuttlecraft when he left.