Part I:
I believe that, despite the seemingly mercurial and boundary-less morality of Peter Pan, there are instances in which he shows himself to have a moral code. Even though he seems less restricted than many, and he is seen by Wendy and the others to be the stereotypical naughty boy, who never wants to grow up and always gets in trouble, he acts according to a code of ethics. He is dedicated to the protection of Wendy and the Lost Boys, and seems to be very kind to those for whom he feels responsible. He saves Tiger Lily from Captain Hook at Mermaids' Lagoon; he does everything he can to save the dying Tinkerbell from the poison, and seems to care very much for both Wendy and Tink, as well as his Lost Boys.
His adversarial relationship with Captain Hook is borne out of that protection; we never get the impression that he would antagonize him for no reason, as he only really wishes to protect Wendy, the boys and other people (e.g. Tiger Lily) from being captured. He places his own life before others in doing show, demonstrating tremendous bravery and courage. He is somewhat selfish at times, but more or less has his heart in the right place. While he does do some things that could be considered amoral (taking the kids away with him to Neverland ostensibly to have more friends for himself, for example), those seems to be anomalies due to his own flighty nature. It does seem much more likely that he would help others than ignore them simply for the sake of inconvenience or whim. Do you imagine that, given the right circumstances, he would leave someone he cares for to die, simply because of his potentially amoral nature? What other choices could Peter have made if he were a bit more capricious and self-serving?
Part II:
The imperialistic and colonialist attitudes of Peter and Wendy are definitely not lost on you - I also got the impression that Peter, Wendy and the boys are all supposed to be 'masters' of this somewhat savage land, with the other groups of people around them having varying degrees of savagery themselves. The closeness in proximity to real sophistication is, indeed, the Indians, due to the appearance of ritual and rite, as well as their own sense of hierarchy; however, they are still looked down upon as not as civilized as Wendy and the others. I do agree, though, that the eugenic hierarchy thing is not presented as an absolute - the people who discuss the savagery of the other Neverland races the most are Captain Hook and his crew, who are undoubtedly shown to be immoral and evil characters; we are not meant to take their opinions seriously.
I agree that Hook's primary strategy for keeping his men in line is through intimidation and military pomp and circumstance. He places himself above his crewmen, so that they might look up to him and he can distance himself from them emotionally. This is vastly different from Peter's outlook, as he considers everyone around him equals, more or less; he incorporates them into his own in-group, and just naturally leads because his charisma and cunning lead him to do so without much thought. Hook has to use much more artificial means to maintain power - the hook on his hand is symbolic of this forcefulness in running his command.
References
Barrie, J.M. Peter and Wendy. Gutenberg Project.
