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You can certainly do it 'by hand' by opening My Clippings.txt and the PDF in question on your computer, and doing some copy/paste to create PDF annotations. And that migration could probably be automated with a script using an open source PDF library (maybe even with a calibre plugin?).
Still it is disappointing that Amazon chose just to mirror their existing annotation features rather than extending it to include support for actual PDF annotations (at least for now). It limits Kindle's usefulness in participating in PDF review workflows, etc., but at least there is something, and hopefully they'll add more annotation features in the future (it would help to have a touch screen for this purpose however).
Sony Reader is way ahead of Kindle in terms of its PDF features, including annotation. But their entire line now has touch screens, so it makes annotation features more accessible and obvious.
That said, there's probably nothing better for portable PDF functionality right now than an iPad.
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