How to disable CMD + E to eject?

You can use Karabiner with a private.xml such as this:

<?xml version="1.0"?>
<root>
  <item>
    <name>Disable ⌘E</name>
    <identifier>DisableCMDE</identifier>
    <autogen>
      __KeyToKey__
      KeyCode::E, VK_COMMAND | ModifierFlag::NONE,
      KeyCode::VK_NONE
    </autogen>
  </item>
</root>