How do I turn off clean URLs only for logged-in users?
This isn't possible in Drupal core because the clean url check occurs so early in the bootstrap phase, i.e. before you would be checking for permissions, settings, etc. One hacky possibility is to try and determine in your settings.php file if a session is open and then enable the clean_url settings dynamically:

$conf['clean_url'] = 0;


But even that would probably be swamped by your htaccess settings and mod_rewrite.