Comment Summary (Score 4, Informative) 238
I did not know it was possible to detect javascript in a PDF, and I think this is possibly a better approach than a full rewrite (btw: I found this python script: http://blog.didierstevens.com/programs/pdf-tools/ ) So instead of rewriting every PDF, you just choose to delete any PDF attachments that are detected with JavaScript. I assume this will then not break any legitimate PDFs that have comments or forms, etc? It will need testing, I guess.
The mail relay can then be configured to detect and delete any javascript-containing PDFs and allow everything else through (including encrypted, which is more likely to be legit than not). Once again, this is not the only protection against this malicious code, but just one facet. I found some recent exploits that don't need javascript at all, so it seems the safest, yet most likely to make you hated, approach is to rewrite the PDF completely or not allow PDFs at all.