Corrigido. Eu usei o seguinte script no KeyRemap4MacBook:
<?xml version="1.0"?>
<root>
<appdef>
<appname>AQUAMACS</appname>
<equal>org.gnu.Aquamacs</equal>
</appdef>
<item>
<name>Switch Ctrl and Cmd in Aquamacs</name>
<identifier>private.appdef</identifier>
<only>AQUAMACS</only>
<autogen>--KeyToKey-- KeyCode::COMMAND_L, KeyCode::CONTROL_L</autogen>
<autogen>--KeyToKey-- KeyCode::CONTROL_L, KeyCode::COMMAND_L</autogen>
</item>
</root>