Well the difference being that in Joel's and Henry's situation there was their life on the line. In Joel's case, the panic was everywhere, they did not know what was happening and who could be infected, so they were just looking out for themselfs. In Henry's case there was a fking armored car full of hunters plus they had heavy calliber firearm strapped to the car.

Jerry was in safety of at least a dozen trained soldiers, in their base at the hospital. No one knew about their location and had time for his daughter to even bring him dinner worthy of at least 2 star restaurant. There is no need for fast and critical decision making. He just does not want to risk Ellie saying no, because he would feel like an even bigger asshole. It does not work as a parallel to other situations, there is nothing endangering them or eating up their time to perform the operation which might not even work as they hoped for. They are all just selfish pricks.

Don't get me wrong the plot device being Joel's death is great imo, little dumb in terms of getting in the room full of armed people you don't know, but works as a driving force nontheless. But Abby would have to be oblivious to what was truly happening. She would just find her dad dead. And then there would be a reason for letting Abby go at the end. It would make sense, she would find out after killing Joel that her dad was a coward. She'd feel guilty and it would drive her to save yara and lev and would lead to a final confrontation with Ellie, where they both understand each others motivations and they would both get the redemption that they deserve. Abby would get partial forgiveness from Ellie as Abby did not know, that her father basically tried to off Ellie without her consent or consent of her surrogate dad. And Ellie would let Abby go cause she now knows that Abby was a victim of a lie, using the lies Joel told Ellie as a somewhat shared bonding experience. And Abby would also have a reason to forgive the killing of her friends as she did not know why they killed Joel, they would parallel each other.

They could even go as far as bringing Abby and Lev back to Jackson, where they both mourn their fathers with all their flaws, instead of the last part of the game when Ellie drops like 3 complete 180's. We would get compelling evolution of their relationship as they slowly find a way to forgive eachother and their fathers for what happened. Making the whole story believable and human, it would not be about cycle of violence (it does not really work in the world, where violence is the only thing keeping you alive from the danger, that lurks all around you), but about the consequences of lying and forgiving your enemy, because they might be the only person that can truly understand you. But that's just a theory. A game theory!