Sometimes there is a need to make drupal redirect using drupal_goto. We had to do it in an SSO scenario. We had to make drupal goto a configurable admin page (node page) when no roles where assigned to you by the external authentication (shibboleth). So we would put a check in hook_init() to redirect drupal when our criteria where met.

This breaks drush. But, there is a solution. You can detect by who php is called using php_sapi_name(). When it is your webserver it will output:'apache2handler', when it is drush it will output 'cli'. In following snippet we check if drush is using php. You also see a check to check on which pages not to redirect, $path could be mapped to admin settings or hardcoded.