This is an interesting question to respond to, because it infers that there was a problem or an issue from which Chris was running, or that made him seclude himself from society. Whilst we can perhaps see that his innate sense of right and wrong was partly responsible for such extreme behaviour, the information that the author gives us concerning his background and the kind of young man that he grew up to be likewise proves to be instrumental in answering this question.
In Chapter 11, the author points towards the extremely complex nature of Chris's character. Note how he describes him as a curious mixture of paradoxes:
McCandless's personality was puzzling in its complexity. He was intensely private but could be convivial and gregarious in teh extreme. And despite his overdeveloped social conscience, he was no tight-lipped, perpetually grim do-gooder who frowned on fun. To the contrary, he enjoyed tipping a glass now and then and was an incorrigible ham.
Another paradox was the way that Chris felt about money. On the one hand, Chris believe that money was "corruping, inherently evil" and yet on the other hand he was a "natural entrepeneur." It seems that one central element of his character therefore was the desire to embrace extremes in every sense. His moral beliefs and view of the world caused Chris to reject the materalism of society and to embrace the transcendentalist notions of self-reliance and a return to nature. When he read the American Romantics, such as Thoreau and Emerson, he had found the kind of extreme example that he wished to follow.
Let us also remember that the discovery of his father's infidelity and previous marriage also turned Chris against him, as this "sin" did not fit in with his strict moral code. Thus, I would argue we need to look at Chris's character overall to find the reason for his isolation from society rather than a specific thing that he was fleeing from.