You can't change the folder structure so that the Canon EOS 450D, or any other Canon EOS camera for that matter, doesn't use subfolders named 100CANON, 101CANON, 102CANON, etc. inside the DCIM folder to store image files. This is fully compliant with the industry standard outlined by the Design rule for Camera File system. This standard was adopted as the de facto standard for storing digital image and sound files in memory devices by the digital camera industry to insure interoperability from one brand to the next.

If others are successfully using the Camera Connection Kit (CCK) with any Canon EOS camera, and indications are that some Canon users have successfully transferred files via the CCK, then the file structure is not your issue.

From wikipedia:

Design rule for Camera File system (DCF) is a JEITA specification (number CP-3461) which defines a file system for digital cameras, including the directory structure, file naming method, character set, file format, and metadata format. It is currently the de facto industry standard for digital still cameras. The file format of DCF conforms to the Exif specification, but the DCF specification also allows use of any other file formats.