The outcome confuses Junior because it defies his expectations.  The merciless manner in which Roger and the other jocks had been bullying Junior indicated nothing of relenting.  Adding to this was that Junior felt fundamentally rotten that Rowdy, the person who had protected him on the Rez whenever he was bullied, was not there. Junior figured that even standing up to Roger would carry consequences that would prolong the harassment and intimidation. Yet, the outcome of Roger retreating surprises and confuses Junior.  He seeks guidance from his grandmother as to why Roger backed away.  Indeed, Grandmother is right in suggesting that Roger's respect was won, something that we see in the way Roger treats Junior as both quality teammate and friend as the novel progresses.  

As for whether Junior is right to punch Roger, this will be dependent on opinion.  Alexie's opinion is that Junior is right for standing up in the manner he did.  Rowdy is not there. Junior is essentially all alone.  No one is there to help him in a setting where he fundamentally challenged without any recourse.  The narrative develops in a way where Alexie feels that punching Roger was the right thing to do.  If one believes that violence in any form is wrong, then Junior probably did the wrong thing in hitting Roger.  Yet, it becomes clear that Roger has a different view of Junior after he is hit, evidenced in how he helps Junior on the team and lending him money for the formal dance.  The manner in which the narrative is developed makes clear that this probably does not happen if Junior does not stand up to Roger in the way he did.