Had he approached Padma in a friendly manner, putting himself on equal footing (instead of trying to teach and impress!), and then told her pretty much the same things he ghost-whispered, it would still have likely redeemed her, except he also would have gained a precious friend and possibly ally (and Hermione's respect). Interestingly, he would also have been following both Quirrell and Flitwick's advice in doing so.
But in any case: "Self-centredness", combined with its cousin Arrogance, is the main flaw that keeps Harry from being a Mary Sue, that keeps him making enough mistakes to allow the story to be unpredictable rather than Harry Steamrolls Everyone (steamroller stories are occasionally fun, but seldom for long). The time, if any, for him to solve that flaw should normally be the final part of the story arc.
FYI: Version 1 of Ch. 50 had Harry approaching Padma directly... and having to be considerably more threatening in order to have a smaller impact on her, which is what got him in trouble with Hermione in the original version.
Version 2 won out over Version 1 because it was weirder, and therefore more awesome; and also because it got him into less trouble with Hermione - I didn't like having her be quite so clearly in the right in Version 1, i.e., so right that even Harry would notice. It had to end on a note of ambiguity from Harry's perspective.
The thing...
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.