The solution adopted by Unix-era GUIs, and the Macintosh, was to use a different key for GUI shortcuts rather than overloading Control. X11 generically calls it ‘Meta’, USB calls it ‘GUI’, Sun had Diamond, etc. It was only Windows that botched it, and the this-is-finally-the-year-of-Linux-on-the-desktop-trust-me-this-time crowd who slavishly imitate it while ignoring Unix experience.