I found out a workaround. The solution is to use the xmodmap utility and make it load a personal file with the correct mapping for the keyboard.
Open a terminal and create a new file in your /home folder, lets call it .Xmodmap
(I use nano as a nice text editor inside the console, you can use Gedit instead, install nano with the command sudo apt-get install nano if you'd like to test it, it's quite obvious to handle.)
Copy/paste the following content to the new file:
keycode 105 =
keycode 206 =
keycode 133 = Control_L NoSymbol Control_L
keycode 134 = Control_R NoSymbol Control_R
keycode 37 = Super_L NoSymbol Super_L
add control = Control_L
add control = Control_R
add mod4 = Super_L
Make the file executable.
chmod +x .Xmodmap
Test it now with the following command:
The dash should now appear with CTRL instead of CMD, hurra!
Now we want the file to be executed each time the system starts up. Open the Startup Applications utility and add a new entry, name it as you want and put the following comand in it:
Reboot, it should be ok. If it is not, you should add a .xinitrc file in your /Home folder, and add the command inside it. The .xinitrc file will be read by the system while loading the desktop environnement.