This converter is reasonable: http://www.willus.com/k2pdfopt/ I wonder if someone has done a Calibre plugin for it.
Looks promising. Hopefully this would also remove javascript and executable code from the source PDF, although any exploits may run within the context of the converter. To be safe, conversion could be run from a livecd.
PDF malware can be used for economic espionage targeting commercial research. What would help is a single open registry which has: bibliographic metadata + hash of known-good PDF for each paper.
Edit: I gave it a test run, and found it does the job very well. Thank you again!