The problem occurs when you have a lot of sites, and do not want *anyone* to run PHP. You have to disable not only the PHP input. But also the ability for people to switch it on. Which means you ghave to seriously restrict all their permissions. Same goes for when you *do* what Joe Moderator of your site to be able to administer certain areas (like users) but definately not to give the the option to run code.

Fair enough, but that seems like something specific to Drupal hosting providers. This would not necessarily be beneficial or desirable for the average drupal administrator running a few sites. I think this could be a good feature to include as an option somewhere, perhaps invoked from settings.php but I think it should be optional, not required.