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Thinking about the citation issue, maybe the thing to do would be to allow auxiliary "page mapping" files to be associated with ebooks. Basically, these would simply map the ereader's internal location system (e.g. Kindle locations) to some other pagination system, e.g. the pages of a particular paper edition. On your Kindle (or other ereader), you would have the option to display the current location in any format your "page mapping" file supports. You could, for example, set it up to track the paper edition(s) you happen to own, so you could go back and forth.
The downside is that, of course, somebody would have to go to the effort to create the "page mapping" files. But if you're trying to sell your ebook for academic purposes, it strikes me that you have a pretty good incentive to create such a file for your purchasers. And I suspect that there would be a community of folks willing to create such mappings simply for their own satisfaction.
The advantage of having a separate file is that it could be swapped/updated at any time without having to obtain a whole new ebook. You could also "retrofit" this solution to ebooks you've already purchased. You could also periodically update your "page mapping" files to include future printings of paper books.
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