How about remapping the keys? xmodmapxmodmap 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:
xmodmap -e "remove control = Control_L"
xmodmap -e "remove mod4 = Super_L"
xmodmap -e "add control = Super_L"
xmodmap -e "add mod4 = Control_L"
This will work until you end your session.
2) Write this into it:
remove control = Control_L
remove mod4 = Super_L
add control = Super_L
add mod4 = Control_L
3) You should now somehow put
xmodmap ~/.Xmodmap to run at startup (I'm having trouble to find out how right now, will fix later).
You can learn more abour xmodmap xmodmap ArchWiki.