Disable the Command-Tab shortcut from Dock
You might use a private.xml like this with KeyRemap4MacBook:

&lt;?xml version="1.0"?&gt;
&lt;root&gt;
  &lt;item&gt;
    &lt;name&gt;test&lt;/name&gt;
    &lt;identifier&gt;test&lt;/identifier&gt;
    &lt;autogen&gt;__KeyToKey__ KeyCode::TAB, VK_COMMAND | ModifierFlag::NONE, KeyCode::F19&lt;/autogen&gt;
    &lt;autogen&gt;__KeyToKey__ KeyCode::TAB, VK_COMMAND | VK_SHIFT | ModifierFlag::NONE, KeyCode::F19, ModifierFlag::SHIFT_L&lt;/autogen&gt;
  &lt;/item&gt;
&lt;/root&gt;


Then remap F19 or shift-F19 in Quark if it is possible.

This would actually disable command-tab and shift-command tab:

&lt;autogen&gt;__KeyToKey__ KeyCode::TAB, VK_COMMAND | ModifierFlag::NONE, KeyCode::VK_NONE&lt;/autogen&gt;
&lt;autogen&gt;__KeyToKey__ KeyCode::TAB, VK_COMMAND | VK_SHIFT | ModifierFlag::NONE, KeyCode::VK_NONE&lt;/autogen&gt;