Assuming you're using Ubuntu 11.10, running the following in a terminal should do the trick:
gsettings set org.gnome.desktop.thumbnailers disable "['application/pdf']"
Alternatively, you can do this in the GUI by installing the
dconf-tools package and running
dconf-editor. In the tree on the left, navigate
org → gnome → desktop → thumbnailers, then edit the
disable option in the right pane as above.
I'm not sure what specific vulnerabilities you are trying to avoid (if they existed, I'd expect you could avoid them by installing the corresponding Ubuntu security updates), but the above should prevent generation of new PDF thumbnails.