However, the syntax isn't quite the same as the usual commands for setting a key to a value.
For Application-specific commands, use the following:
defaults write com.developer.app NSUserKeyEquivalents -dict-add "Menu Item" -string "@$~^k"
The meta-keys are set as @ for Command, $ for Shift, ~ for Alt and ^ for Ctrl. k in this example is the non-meta-key that you want to use.
For system-wide shortcuts, you can use -g instead of the app identifier, e.g.
defaults write -g NSUserKeyEquivalents -dict-add "Menu Item" -string "@$~^k"
Note that you'll need to relaunch the app before these will take effect. Also you can see if they've been successful in System Preferences -- which will also need a relaunch to show the changes.