Andrew – a similar problem exists with WordPress. If a user of WordPress wants to edit their template files via the backend they must edit php files – those files have to be owned by the webserver, just like WPMU template files.
In a WPMU install, the directories that are world writeable (or preferably owned by the webserver) only hold Smarty code/html or images, no PHP. Right now of course there’s no advantage as Smarty has to be running in secure mode and by default that’s not enabled.