User a terminal and make the directory
mkdir -p ~/.config/indicators/messages/applications-blacklist/
Files in here should be paths to .desktop files which will be blacklsited on startup. The .desktop files in question are located in
/usr/share/indicators/messages/applications
so you can make symlinks from there to this directory. Thus
ln -s /usr/share/indicators/messages/applications/menuItem ~/.config/indicators/messages/applications-blacklist/menuItem
will remove menuItem
from the messaging menu. Run
ls /usr/share/indicators/messages/applications
to see what the names of the .desktop files are and look for the one mentioning Ubuntu One.
You can run
killall gnome-panel
to see the changes immediately. Else, a logout should work as well.