you got me thinking about this issue.
It does seem better to me if the user is not an admin or high priveledge user it would be better to not let them wander the whole file system beneath /Data/Sites/[SiteID]/
but to constain them to a folder that is just for media, images, flash movies , downloads etc.
So I'm introducing a new folder at /Data/Sites/[SiteID]/media/ and users other than admin will be restricted to managing files (in the editor) beneath that folder. They can still create folders and organise as they need.
Admins and Content Admins will still be able to navigate from the root of the site folder, but other uswers with edit roles will be constrained to the media folder.
This may introduce a backaward compatibility issue where file sneed to be copied beneath the media folder so that they can be browsed by content editors as before.
I will also make a web.config setting so its easy to force allowing the site folder as root for backwarcd compatibility.
I will make these changes for the next release.