i honestly dont know who killed him it isn't made very clear it seems to be Arthur's father but i have heard people suspect it is Isabelle or even Violet Hart maybe that will be answered in a future episode
John: You took my gun, didn't you? Your father didn't kill Lucille-- *Isabelle: My father was too weak. She would have ruined our family. *John: Your father wasn't the one who shot me. *Isabelle: I had to do it. Do you understand? *John: You tried to kill me! *Isabelle: I didn't have a choice!