The difference between Chris's father, Walt, and the author Jack London, aside from their personal and moral ideals, is that Walt was simply too close a figure for Chris to view objectively. Living with Walt for most of his life, accepting Walt's authority while secretly blaming him for serving society's ideals, Chris developed a mental relationship with a peer figure, London, setting an impossible standard for his father to reach.
Like many people, Chris apparently judged artists and close friends by their work, not their life, yet he was temperamentally incapable of extending such lenity to his father... Chris would fixate on his father's own less than sterling behavior many years earlier and silently denounce him as a sanctimonious hypocrite.
(Krakauer, Into the Wild, Amazon.com)
Since London had been dead for years, Chris didn't have to dwell on the author's personal failings; he could look at London's writings and interpret them as he pleased. His father's authority was too personal, too direct, for Chris to ignore; he ended up resenting Walt's personal mistakes (such as carrying on an affair with his first wife) even more than the attachment to society. Chris held people up to the pedestal he created for London, Twain, Tolstoy, and Thoreau, and was unable or unwilling to view his father objectively.