Exclude all sticky posts front page twenty twelve

Don’t use query_posts. Use a filter on pre_get_posts.

function no_front_sticky_wpse_98680($qry) {
  if (is_front_page()) {
    $qry->set('post__not_in',get_option( 'sticky_posts' ));
  }
}
add_action('pre_get_posts','no_front_sticky_wpse_98680');

By running query_posts you clobber the main query, over-writing it with another query. That is why you break pagination. The new query gets out of sync with what should be the main query.