I think the big thing you're missing is that Flint's emotional motivation needs to be tied up in Piracy As Revolution, and him being gay long before it's accepted, and persecuted for it, is a great way to tie emotionality to his politics. Flint is nothing if not intensely passionate about his goals to burn The Old World down, and I wouldn't want to lose that fire for something more stoic and pragmatic. Flint's impassioned anger towards the world makes the show work. He becomes The Monster long before Miranda is killed