The 'positive' word that came to mind is freethinker which I found defined as
a person who forms opinions on the basis of reason, independent of authority or tradition [...]
Collins Dictionary gives a very similar definition:
"Independent of authority" is the part that fits your case.
Free thinking has historically been considered a defiance of authority in itself because the independence of the mind is the first step towards other forms of independence. Moreover a freethinker encourages others (who come into contact with him) to reject 'received wisdom' and think critically for themselves, which is considered a direct challenge to traditional forms of authority.
At heart, I am a freethinker.
(Oh yes I am, even though I don't go and deliberately challenge anybody's authority!)
Note: the exhaustive list of synonyms of 'rebel' at http://www.thesaurus.com/browse/rebel does not seem to contain a single word whose meaning is commonly understood in a 'positive sense.' That tells you that society does not like a person or group that questions authority. In the context of armed resistance or revolution I have heard it said that
One man's rebel is another man's freedom-fighter.