we can easily do this witht the below peace of code. It will add a new option to the existing attribute.
$arg_attribute = 'your_attribute_code'; // enter your attribute code here
$arg_value = 'new option value';
$attr_model = Mage::getModel('catalog/resource_eav_attribute');
$attr = $attr_model->loadByCode('catalog_product', $arg_attribute);
$attr_id = $attr->getAttributeId();
$option['attribute_id'] = $attr_id;
$option['value']['any_option_name'][0] = $arg_value;
$setup = new Mage_Eav_Model_Entity_Setup('core_setup');
$setup->addAttributeOption($option);