I just stumbled upon the very same problem that Omar described. Here's a guide that I hereby commit to let others get help, just remember to back-up your files first! The same goes about your WP-database, of course.
2. Delete every file in the root, that starts with "wp", except for
3. Upload the WordPress 2.3-folders and files for
wp-includes, followed by all the files in the root.
4. Go to http://your_domain/wp-admin/upgrade.php and follow the instructions.
Presto! Now your database should be updated and WordPress 2.3 up and running!