Since EPUB is much more accessible to blind/visually impaired people than PDF, perhaps the federal government could step in and mandate that all articles with content produced using federal grants must be available in a format that the blind/visually impaired can consume as well.
0: http://scholarlykitchen.sspnet.org/2013/03/19/is-it-time-for...
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!
I tried all sorts of other things, but this was the least painful.