What the fuck were you doing with your life when Assassin's Creed Black Flag came out? I pretty much rocked drunken sailor on repeat when sailing the seas.
The "captain's daughter" was a euphemism for the cat o' nine tails. So in other words, that line meant give the drunken sailor a lashing as punishment.
Isn’t it: put him in the hold with the captains daughter? And there I thought captains daughter was slang for a cat o’ nine tails, which was a type of whip. Though if they put him in the hold with the captains actual daughter, that might be a good way to get a guy killed.