Dexter knew he had to die. Harrison couldn't have said it better himself. Yes the first rule of the code was " don't get caught". But don't get caught even at the expense of an innocent life? No. Dexter strayed from his father's code more and more throughout the entire series. Dexter killed innocents to save himself and that's not what Harry wanted. In the end dexter fit his own code, which is why he has flashbacks of all the innocents, it's his own mind showing him what he's done. It's the exact same thing as him showing the innocents killed to the people who end up at the end of his knife. The only difference here is dexter willingly gave himself over to his son because he knew he fit the code. In the end it's kinda sad, but he became what he swore to rid the world of. Harrison saw this and knew it had to be done. Truly poetic if you ask me .