Same as you. Ben in the bell tower. I hated him for getting so many people (that telltale suckered me into caring about) killed, through both stupidy (forgivable) and cowardice (not so forgivable) and i wanted the Molly to take his space on the boat.
I was basically hoping/looking for a chance to kill him, but then when it came it felt so harsh and i wasn't gaining anything by killing him. I paused the game for more thinking time i was so conflicted.
Eventually dropped him.