Is there a way to add a persistent querystring across multiple pages?
The way I would go about this would be to dedicate an alias subdomain and perform the redirect before hitting the application.

For example, Apache can be configured via mod_rewrite to add any query parameter to the requested URL:

  # Add iframe=1 to query parameter if requested from iframe domain.
  RewriteCond %{HTTP_HOST} ^if.example.com [NC]
  RewriteCond %{QUERY_STRING} !iframe=1 [NC]
  RewriteRule ^(.*)$  http://if.example.com/$1?iframe=1 [L,R=301]


The only problem this causes is that D7.5 now forcing iframes to only originate from the same domain so you'll have to explicitly allow iframing from this different domain in your settings.php:

# Allow iframing on host requests to the iframe domain
if ($_SERVER['HTTP_HOST'] == 'if.example.com') {
  $conf['x_frame_options'] = '';
}