i have no prior experience in this area but your post got me interested. i know only "secure" and "directory level access control" as your requirements. more info might help others to suggest better alternatives (such as file size, read-only access to users? etc.)
what about hosted CVS/SVN/VSS like products such as
CVSDude: Professional CVS Hosting and Subversion Hosting
Also will this URL be useful?
File Hosting Review: Data Storage Services