Say you want to remove the body field from the page content type. Putting this code inside an updatescript will get the job done. Remember not to use field_delete_field() if you're not sure if you still want to use the field anywhere else. It's way safer to rely on field_delete_instance. Setting the second parameter to TRUE means it's automatically going to clean up the field anyway if it is found to be the last instance.
$instance = field_info_instance('node', 'body', 'page'); field_delete_instance($instance, TRUE);