Well it turns out that those driods that let Obi's twin escape were still working on my ship despite my orders for them to be turned to scrap, it seems that the droid I gave the order to "forgot" to tell another droid to get them to be terminated.

Anyway they thought Jedi Master K'Kruhk was dead, it was a quite mutilated corpse, and decided to bin it, I walked into the cell, saw the Jedi missing, and slew every droid on my way to the hangar where I promptly borded a landing vessel and left the ship.

Hey Master Sidious I've found a target to test the Death Star on! Now I have to find a new ship.