Then do this:
1) Run the program, then exit.
2) cd ~/Library/Preferences
3) cp net.sourceforge.iTerm.plist net.sourceforge.iTerm.plist.bak
4) plutil -convert xml1 net.sourceforge.iTerm.plist
5) edit the plist file, and find this section:
<key>Global Profile</key>
<string>Yes</string>
<key>Key Mappings</key>
<dict>
6) Insert the following after the <dict> (I wrote this with an Emacs macro after doing the first three by hand in the keyboard profile editor...) :
<key>0x61-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>a</string>
</dict>
<key>0x62-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>b</string>
</dict>
<key>0x63-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>c</string>
</dict>
<key>0x64-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>d</string>
</dict>
<key>0x65-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>e</string>
</dict>
<key>0x66-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>f</string>
</dict>
<key>0x67-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>g</string>
</dict>
<key>0x68-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>h</string>
</dict>
<key>0x69-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>i</string>
</dict>
<key>0x6A-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>j</string>
</dict>
<key>0x6B-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>k</string>
</dict>
<key>0x6C-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>l</string>
</dict>
<key>0x6D-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>m</string>
</dict>
<key>0x6E-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>n</string>
</dict>
<key>0x6F-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>o</string>
</dict>
<key>0x70-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>p</string>
</dict>
<key>0x71-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>q</string>
</dict>
<key>0x72-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>r</string>
</dict>
<key>0x73-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>s</string>
</dict>
<key>0x74-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>t</string>
</dict>
<key>0x75-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>u</string>
</dict>
<key>0x76-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>v</string>
</dict>
<key>0x77-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>w</string>
</dict>
<key>0x78-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>x</string>
</dict>
<key>0x79-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>y</string>
</dict>
<key>0x7A-0x100000</key>
<dict>
<key>Action</key>
<integer>10</integer>
<key>Priority</key>
<true/>
<key>Text</key>
<string>z</string>
</dict>
7. Save the file, then restart iTerm. All Command keys will now be remapped to their Alt equivalents. This has the side effect of completely disabling all the menu commands, but if you're like me you really won't give a rat's ass. :-)