All I know is that Joel chose what any father wouldNah.
Nobody's whose making the choices is clearly right in that situation. They're all willing to murder for their own selfish desires towards what they consider to be ultimately noble ends. It's literally the Tolly Car dilemma. That's why it's a philosophical dilemma, there is no good answer. The Fireflies are willing to kill one to save many, and Joel is willing to kill many to save one whom he cares about. Both are morally and ethically questionable. That's part of what makes it interesting.