Yeah, so I don't think a human killed Otohime. I believe it was Decken, because he had a rifle. And Jones just took advantage of the situation by taking random human pirate, smashing his face in and yelling to the citizens that he found the murderer, promoting his hate towards humanoid people. Decken probably did it to get all attention to Otohime, so he could sneak up at Shirahoshi.
So, who do you think killed Otohime?