A crude solution is already possible:
http://code.google.com/p/minify/wiki/CustomSource#Example:_Content_from_a_URL

But something that would be resilient to remote errors is forthcoming, with usage
looking something like: (in groupsConfig.php)

$src1 = new Minify_Source_Url(array(
  'url' => 'http://3rdparty.com/file.js'
  ,'contentPattern' => '@if this doesn\'t match, use backup@'
  ,'backupFile' => '/path/to/file_backup.js' 
  /* many more options */
));

return array(
  'js' => array('//js/file1.js', $src1, '//js/file3.js');
);

Great! Looking forward for true integration with Minify. 

(Offtopic: Thank you for making this great script, I've reduced HTTP requests from
16 
to 2!)