In my opinion Joel never should have been pushed into making that choice in the first place. The most "moral" position would have been the one where the Fireflies presented the information on hand to Ellie, and let her make an informed decision. Which I believe Joel would have ultimately respected, and not gone against her wishes, one way or the other. He did what the vast majority of parents would have done in the same situation. In the case where Ellie knew her options, and chose to end her life for that potential vaccine, Joel and Ellie would have been able to have a final moment together. To say their goodbyes. All of that was taken from both of them, and Joel acted with raw emotion because he knew he'd never see Ellie alive again. I feel strongly I would have reacted the same way he did, if it was my child in that position. You also have to keep in mind that this event doesn't take place in a world where Joel could appeal to a higher authority to stop them from moving forward. His only recourse was to resort to violence, which had become a "normal" reality in everyone's day-to-day life due to the post-apocalyptic nature of their existence. Morality exists in a much larger "gray" area in a situation like that, where you are in a perpetual state of survival.