That's easy to fix. Use iTerm2, and tell it to remap modifier keys (to unflip them). If you use mission-control shortcuts (like move workspace), configure those keys in iTerm2 to "don't remap modifiers"
@leephillips - good news is that linux installs fairly painlessly on the iMac 5K. I'm running Fedora 20 and it's going really well. Some slight funkiness with sound but I'm sorting that out now.
Need hardware accel for gnome shell so required this workaround for the ATI drivers: https://bugzilla.redhat.com/show_bug.cgi?id=1054435