How about remapping the keys? [xmodmap][1] should do the trick there.

Assuming that your command button is replaced with meta (I can't help you there, I don't own a Mac) this should work for you:

<code>xmodmap -e "remove control = Control_L"
xmodmap -e "remove mod4 = Super_L"
xmodmap -e "add control = Super_L"
xmodmap -e "add mod4 = Control_L"</code>

This will work until you end your session.

**Permanent solution**

1) Make <code>~/.Xmodmap</code> file.

2) Write  this into it:

<code>remove control = Control_L
remove mod4 = Super_L
add control = Super_L
add mod4 = Control_L</code>

3) You should now somehow put <code>xmodmap ~/.Xmodmap</code> to run at startup (I'm having trouble to find out how right now, will fix later).


  [1]: https://wiki.archlinux.org/index.php/Xmodmap