You can customize the command keys used for an individual application in System Preferences > Keyboard & Mouse > Keyboard Shortcuts. I think (if I understand correctly what you're trying to do) that this might allow you to accomplish your goal. You could remap all of Terminal's command keys to use control instead of command, to get them out of your way... but then you might need to do a lot of customization on the machines you ssh into, so that they use Command instead of control
It seems that you're going to have to do an ENORMOUS amount of work just to allow you to use your pinky instead of your thumb for the modifier key.
Another possibility: user preferences can be manipulated by the "defaults" command. I haven't been able to find a way to use this to control they modifier key mappings, but it should logically be possible (if you're willing to do a lot of digging). If so, then you could write short scripts to switch back and forth between Mac default and your swapped mode. Trigger the scripts with Quicksilver, and whenever you use Terminal you can call one script, and whenever you leave it you can call another. Again, a big pain to achieve what you want, but it might be possible.
I don't think there's a clean and simple solution.
I've seen third-party programs that give more control over manipulating modifier keys, if you're willing to install them (probably kernel extensions). They might be able to do what you want, but I don't recall the names. If you google for programs to fix emacs and vi keys you might find them.
Good luck.