In addition to Krakauer's book and Penn's film, there is another source of information.  Chris McCandless' sister Carine recently wrote  "The Wild Truth."  She includes information that provides insight into what prompted her brother to go  into Alaska, and answers some of the questions.  In an introduction to her book Krakauer states that he downplayed or left out some elements of the story, evidently a a price for her cooperation with "Into the Wild."

What was left out included violent spouse abuse, with the siblings huddled while the parents fought, night after night.  In addition, the father had a second parallel family, and both families spent vacation time together.  The children resented that they were required to put on a "show" as a perfect family, knowing that reality was much different, even criminal.  

Another element is that months or years later a backpack in the bus produced McCandless' passport and some money, perhaps indicating that he indeed intended a return.