You can conceivably use PDF protection to prevent the Illustrator from being used as a PDF editor, making it non-editable unless a password was provided. However, that would prevent you from creating PDF/X since the PDF/X standards do not permit PDF protections to be applied. (In theory, this could have be allowed in the PDF/X specifications, but the “print industry” felt that even simple protections such as not allowing editing would make PDF usage too inconvenient for them.) And you really do want to use PDF/X (and in particular PDF/X-4) for PDF print publishing workflows!
Unfortunately, the only remedy for the problem of users,
including prepress professionals who should know better, opening PDF files in Illustrator is (1) education and (2) a “written” (in e-mail) warning with every PDF file you send that opening a PDF file in Illustrator is a lossy operation that could corrupt the contents.
FWIW, the same issue is associated with users opening PDF files in Photoshop. I've recently heard of some prepress operator who takes every PDF file exported from InDesign and opens same in Photoshop, resaving as a PDF file from Photoshop and printing that, then complaining about spot color and quality issues!
- Dov