The option as meta key selection has no effect on the Command (Apple) key.  If option as meta key is selected, then the Option key acts as a Meta key in bash and elsewhere; just press Option-F.  If you de-select it, then there is no Meta key.
If you are running OS X 10.6 (Snow Leopard), Apple supplies a built-in way to change the meaning of the keyboard modifier keys, including Command and Option.  Go to System Preferences -> Keyboard and click on the Modifier Key... button.  A panel will appear that allows you to, for instance, swap the meaning of the Option and Command keys.  But, be warned that this is a global option and will apply everywhere on OS X and could lead to some major confusion.  If you do that, you will be swimming upstream as noted here.  You will likely be best served long-term by getting used to the OS X default of using the Option key as Meta and, if necessary, restoring application defaults (for Emacs, say) to follow that convention.
FURTHER EDIT:  This blog post and program (untested) might be helpful.