I just installed Debian on a mid-2012 MacBook Pro and encountered the same problem after looking around for a while. I am very new to this whole Linux business and StackExchange, so bear with me. If you are not familiar with MacBook keyboard like myself, you can use xev to find out their names, keycode, etc.
My keyboard has a similar setup:
[fn] [ control ] [alt/option] [⌘ command] [space] [⌘ command] [alt/option]
Using xev, this is equivalent to:
[fn] [Control_L] [ Alt_L ] [ Super_L ] [space] [ Super_R ] [ Alt_R ]
Under /usr/share/X11/xkb/symbols/, you can modify the mapping on different levels, for this answer, I'll just stick with pc.txt. In it, you'll find something like:
key <LFSH> { [ Shift_L ] };
key <LCTL> { [ Control_L ] };
key <LWIN> { [ Super_L ] };
...
key <RTSH> { [ Shift_R ] };
key <RCTL> { [ Control_R ] };
key <RWIN> { [ Super_R ] };
key <MENU> { [ Menu ] };
...
key <ALT> { [ NoSymbol, Alt_L ] };
include "altwin(meta_alt)"
Then I just swap Alt_L and Super_L, then save, reboot.