Dude, since when has government ever followed its own laws? In fiction or RL? It wouldn't be a stretch to say the turian military was working on AI technology clandestinely.
So the turian military was experimenting with making AIs and installed one in the ship. And it being an AI, it would naturally try and save itself when the Gov tries to decommission it along with the ship, so it stored portions of itself within the ship's software/hardware and 'played dead' until the ship was reactivated.

Not saying we should do this obviously, just that it could be a reason why the ship has an AI if it did, which it doesn't. 
So ignore my ramblings.
:p