Use this: wp_delete_term
Edit:
Did a little dig around. With custom taxonomies, if you delete the term, the posts will not be assigned a new one. With ‘category’, whichever you set as the default from ‘Writing Settings’ will be assigned to the post. Besides, if you want to set the default category from code, use update_option('default_category', '<category name>'). There’s a third argument with wp_delete_term, using which you can force a default category, but I really couldn’t find how to use this argument.
(Ref: ../wp-includes/taxonomy.php, l. no. 1681)
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