Abby's revenge is far less justified than Ellie's. She knew that her father did something wrong, she knew why Joel did what he did, she knew that her father in Joel's situation would have done no different. If you know all this and your response is to brutally torture and murder this person, who after all had just saved her life from zombie infected...then I am sorry I can't buy the game's shameless manipulation to make her work.
For some of us, the issue isn't the conceit (i.e. making you sympathize and potentially forgive a villain), it's the execution and presentation. You can't present a flashback like what they did with Abby and her father, and then expect people to walk away saying, "this is the same thing" because it's not.
At the age of 14, Ellie was going to be cut open by Abby's quack father for the vague possibility of a vaccine, in flagrant violation of basic procedures, norms, and ideas of medical science.