Karabiner's “Change left command key to left control key (only in Terminal)”, improved with exclusions for common OS X global hotkeys.

private.xml

<?xml version="1.0"?>
<root>

  <modifierdef>PHYSICAL_COMMAND_L</modifierdef>

  <item>
    <name>Change left command key to left control key (only in Terminal)</name>
    <appendix>+ Retain command-space (Spotlight)</appendix>
    <appendix>+ Retain command-tab (app-switch)</appendix>
    <appendix>+ Retain command-` (window-switch)</appendix>
    <appendix>+ Retain shift-command-/ (menu-search)</appendix>
    <identifier>remap.left_command_to_left_control_terminal</identifier>
    <only>TERMINAL</only>
    <autogen>
      __KeyToKey__
      KeyCode::COMMAND_L,
      KeyCode::CONTROL_L, ModifierFlag::PHYSICAL_COMMAND_L,
    </autogen>
    <autogen>
      __KeyToKey__
      KeyCode::SPACE, ModifierFlag::CONTROL_L | ModifierFlag::PHYSICAL_COMMAND_L,
      KeyCode::SPACE, ModifierFlag::COMMAND_L,
    </autogen>
    <autogen>
      __KeyToKey__
      KeyCode::SPACE, ModifierFlag::SHIFT_L | ModifierFlag::CONTROL_L | ModifierFlag::PHYSICAL_COMMAND_L,
      KeyCode::SPACE, ModifierFlag::SHIFT_L | ModifierFlag::COMMAND_L,
    </autogen>
    <autogen>
      __KeyToKey__
      KeyCode::TAB, ModifierFlag::CONTROL_L | ModifierFlag::PHYSICAL_COMMAND_L,
      KeyCode::TAB, ModifierFlag::COMMAND_L,
    </autogen>
    <autogen>
      __KeyToKey__
      KeyCode::TAB, ModifierFlag::SHIFT_L | ModifierFlag::CONTROL_L | ModifierFlag::PHYSICAL_COMMAND_L,
      KeyCode::TAB, ModifierFlag::SHIFT_L | ModifierFlag::COMMAND_L,
    </autogen>
    <autogen>
      __KeyToKey__
      KeyCode::BACKQUOTE, ModifierFlag::CONTROL_L | ModifierFlag::PHYSICAL_COMMAND_L,
      KeyCode::BACKQUOTE, ModifierFlag::COMMAND_L,
    </autogen>
    <autogen>
      __KeyToKey__
      KeyCode::BACKQUOTE, ModifierFlag::SHIFT_L | ModifierFlag::CONTROL_L | ModifierFlag::PHYSICAL_COMMAND_L,
      KeyCode::BACKQUOTE, ModifierFlag::SHIFT_L | ModifierFlag::COMMAND_L,
    </autogen>
    <autogen>
      __KeyToKey__
      KeyCode::SLASH, ModifierFlag::SHIFT_L | ModifierFlag::CONTROL_L | ModifierFlag::PHYSICAL_COMMAND_L,
      KeyCode::SLASH, ModifierFlag::SHIFT_L | ModifierFlag::COMMAND_L,
    </autogen>
  </item>

</root>