Auto upgrade to 3.0.4 gives fatal error

Hi guys. We’ve been using wordpress for our e-commerce site – https://www.thebabycakery.co.uk – since 2009. Never had a problem upgrading until now. We did an automatic upgrade to 3.0.4 which said it was successful, but when visiting the site it displays this fatal error:

Fatal error: Cannot redeclare is_taxonomy() (previously declared in /home/newbaby1/public_html/wp-includes/deprecated.php:2515) in /home/newbaby1/public_html/wp-includes/taxonomy.php on line 103

I have the site backed up from the previous upgrade, but don’t want to start replacing any files via ftp in case I do more damage. I’m a graphic designer not a programmer so would appreciate some help rather urgently.

Thanks