Use cmd-key-happy
* cmd-key-happy — swap cmd and alt keys in Terminal.app
* cmd-key-happy in github
When it is installed, it starts automatically even in restarting OS X.
It uses ~/.cmd-key-happy.lua script. When it is modified, rerun it by cmd-key-happy-restart.
RT @BreadNCup Bread & Cup Blog: Disabling Command Key in Terminal.app in MAC OS X for Emacs. http://bit.ly/blIREP