How do you permanently remove default rewrite rules from the wp_options table?

Rather than modifying stored rules it would be more reliable to modify rules before they are stored.

• flush_rewrite_rules() calls
• WP_Rewrite->flush_rules()
• WP_Rewrite->wp_rewrite_rules()
• WP_Rewrite->rewrite_rules()

Inside last there are fitting hooks to modify rules (after which result they will be saved as usual on each flush):

do_action_ref_array('generate_rewrite_rules', array(&$this));
$this->rules = apply_filters('rewrite_rules_array', $this->rules);