It comes fast and without context and it's hard to avoid the feeling they spend the rest of the game trying to convince you it made sense. I'm not even sure he had it coming - nor am I convinced that he is as bad as Abby and Ellie.
Ultimately, he made a heat of the moment decision that he wrestles with for the rest of his life, an impossible decision that he would likely have walked away from with honor had that guard not goaded him so openly. Given the historical pretext with Sara (which is glaringly invoked in the final scenes) Joel's choice to rescue Ellie is never one that can be justified, but is at least an entirely human one.
Ellie and Abby, meanwhile, held grudges for months and years at time respectively, dragging their loved ones into their bloodlust at a terrible cost. Not to save lives, as Joel did, but to deliberately extinguish more. By the end, I still liked Joel and felt that his debts were settled. Abby and Ellie though, they're irredeemable psychopaths whose hard-ons for revenge ruined the lives of everyone around them. There's no subtext to drive their irrationality (neither are ever faced with losing another father figure), and their every action is sober, calculated and well-considered. They shed blood in the pursuit of shedding more and never stop to entertain a less selfish path (as Joel did). Perhaps worst of all, it's never in the defense of another - it's nothing but a hollow attempt to reverse the irreversible.