Over on his weblog, Jim Henley asks some pointed questions about how Ditko's well-known Objectivist philosophy meshed with the famous theme of "With great power, there must come great responsibility." Well, one answer is that it didn't. Ditko quit the company, remember — and while a lot of that was because he felt the publisher was reneging on promises of financial participation, some of it was certainly because he felt that he was basically writing the stories and drawing them, and that Stan Lee was then warping what he wrote with the dialogue, occasionally requiring that panels be redrawn to take the story in a slightly different direction. There are a couple of other things that could be said to clarify what seems like a conundrum to Jim, and I say all this having interviewed just about everyone at Marvel in those days who could be interviewed, and even spending an afternoon or two with Ditko.
Both might deny it today but I sure got the impression that at the time, Ditko wasn't quite as militant in his beliefs as he later became and that Lee wasn't all that Liberal. Lee was a lot less Liberal than Jack Kirby, which prompted many an argument, especially when Jack thought he was writing the story and Lee, in the dialogue stage, altered an important (to Jack) underlying philosophy. Someone once made the interesting remark that when Stan worked with Kirby and Ditko, he was caught in the middle: Too Conservative for Kirby and too Liberal for Ditko.
Also, it's been many years since I read any Ayn Rand, but I doubt she would have argued with the basic wording that "With great power, there must come great responsibility." She certainly recognized that, if only as a basic function of nature, some people do have a lot more power than some other people and must decide how to deploy it. She probably would have disagreed with the customary way in which those reponsibilities are generally interpreted in comics, placing an obligation to one's self much higher than any duty to society. But she would not have denied that there was great responsibility to be considered, and I'm not sure that if you take the Ditko Spider-Man stories as a finite set (i.e., don't view them through the prism of later issues), there's that much conflict. Ditko did later concoct several heroes who, though more openly spouting Rand-style views, still put on masks and went out to fight crime. Even Objectivists think it's a good idea not to have violent criminals roaming the street and I don't know that you can always separate that mission from one of pure altruism.
For that matter, the notion of Spider-Man as a wimpy anti-hero is more an invention of Marvel's press coverage than of anything in the published comics, much like the oft-cited but non-existent scene where the hero can't go to his prom and/or go out and duke it out with the villain due to acne problems. That was mentioned so often in articles about Marvel that Stan once called to ask me which issue he'd done that in, and was surprised when I told him, "Never." I don't believe the Lee-Ditko Spider-Man had "feet of clay." He had doubts and worries (mainly in the dialogue, not in the elements Ditko contributed) but apart from a couple of selfish moments in his origin story, he never backed down on confronting Dr. Octopus or the Green Goblin…or questioned that the bad guys were the bad guys. Ditko may even have rationalized the occasional thought balloons of self-doubt as reflecting the kind of confusions that any growing boy experiences before coming to the "right" way to look at the world. And then at some point, along with the money situation, it became intolerable for him.
I can't speak for Ditko. Haven't talked to him in more than twenty years, in fact. But I think the answer can be found in just reading those issues of Spider-Man and looking at the hero's actions…and remembering that the word balloons are Stan talking, not Steve.