Yes, just delete it. That folder is only created when you install Vista (upgrade or over-the-top install) and don't do a format first. Deleting it will harm nothing. You might want to go through it and make sure you have everything you want from it before deleting (document, pictures, etc).
One more thing, if there were any programs that you had installed previously and haven't re-installed yet you can try running them from the exe in the programs folder. If they run you won't need to re-install them, just create a shortcut on your desktop (or add it to the start menu). You can then either leave the program's folder there or move it to the new Programs Folder.