No, you don’t need to reinstall WordPress from scratch, you just need to replace your install of WordPress to reinstall it.
If you do in fact have WordPress 3.0 installed and it is just a tad broken, you might be able to just got to “Dashboard / Updates / Re-install Automatically” and reinstall right through WordPress.
But before you do anything, make very certain you have a good full backup of your site, especially the database.
Within CPanel you should be able to use phpMyAdmin to backup your database.
After you have a backup of your database, you need to access your site via ftp and backup your files. What you want to backup is your wp-content folder, this is where your uploads folder and theme is.
Then, if you have to, you can reinstall WordPress manually by deleting the wp-admin and wp-includes, and deleting the files in your root folder: index.php, wp-activate.php, etc.
Be sure to not delete your wp-config.php file, you need that to connect WordPress to your database, be sure to backup that file.
As long as you have a good complete backup, you can’t really do any damage, but reading through the Installing WordPress documentation will help you with reinstalling your site.
