This is my opinion and not based on research.
What you made is a mistake. We all make mistakes and I can forgive them, especially if I did not lose any money over it. (If the book had not been free and you had refunded your customers it would not have been a big deal either.)
I don't see any reason why I should not give your next book a chance to entertain me. The only thing that would keep me from buying your next book is bad writing.
I don't see a need for you to choose a different pen name. Act as if it had never happened. I have seen many books from major publishers printed or bound the wrong way, and all I did was just not buy them. No problem, no bad feelings.
Only if someone comments on it to you directly should you reply to it (with wry, self-deprecating humor), but do not (ever) reply to reviews; they are not addressed to you. (Reviews are not an invitation to the author for discussion and you must graciously accept them.)
I would recommend that you register at kboards and ask there, too. Members of that Kindle publishing forum have lots of experience with ebook publishing and will have a better idea of the effects of your blunder and a good strategy to deal with it. I'd not be surprised if someone there has had a similar experience.
If you do ask there, please link to that thread in your question, or summarize the advice you get in your own answer here.