It's a basic program, which does not seem to save any settings at all, so I believe it is a totally portable solution.iSafePDF is a free open source PDF protection software.
it allows you to encrypt PDF document, signe them using a certificate and timestamp the signature.
all those features are PDF standards so your document will be readable/editable with all standard PDF programs.
The software can be downloaded at http://isafepdf.eurekaa.org/download-isafepdf/