Jul's death is the only thing that comes to mind for me too—both for where it takes place in the story and that it happens so quickly, and regarding the question of "would this have been fun for the player."

You could have just stuck him in a final chamber and made him slightly tougher than the average Elite and I don't think we'd have lost anything—have Locke deliver the coup-de-grace with a button prompt or a cutscene at the end.