I don't think that Chris McCandless is a true rebel. He socially distances himself from others, because he prefers to be alone, but I don't think that he is a rebel. He's an all around nice guy, which is evidenced by the number of the people that deeply cared for him. It was few people by his own choosing, but they all genuinely liked Chris. If he was some kind of hardened rebel, he wouldn't have been so well liked.
However, Chris does have his moments where he displays rebel tendencies. Chapter 1 has a good example. Chris is hitchhiking his way to the Alaskan interior, and Jim Gallien picks him up. At one point in the ensuing conversation, Jim asks Chris if he has a hunting license. Chris (Alex at this point) responds with a terse sentence.
“Hell, no,” Alex scoffed. “How I feed myself is none of the government’s business. Fuck their stupid rules.”
Because Krakauer put that in the first chapter, I initially thought that Chris was a definite rebel of sorts. A few chapters later, the reader learns that Chris would even intentionally put down false information on his tax documents. Not just false information about his earnings, but fake names and birth dates. Chris flat out doesn't want the government involved in any part of his life. So in that light, he is a strong rebel.