You need to say that the Captain killed everyone, just pick the axe to make it easiest (it's near the top and nobody died from the axe), and you will still list his own death by suicide. He's the only one you need to identify, the cause of death is the important thing. This of course means you will be pretty far into the game to open up every page other than the Bargain chapter. It's easiest to choose the means of death for each person you find as you go. This will also likely net you the
and the final tally should be 57 crew killed by the Captain. Fear not, you can select Begin after the credits and go back to the ship and solve everything correctly.