How to run commerce_order_save() without triggering any rules?
It's possible, but the change would need to be sitewide (not just in the context of rules). You'd need to override the entity controller class used for commerce_product (which you could do with hook_entity_info_alter()), and re-implement its save() method so it doesn't invoke the entity hooks.

If that is undesirable (probably is), and you just need to update field values, you can use field_attach_update() instead, which will bypass the entity save process altogether:

$order-&gt;some_field[LANGUAGE_NONE][0]['value'] = 'foo';
field_attach_update('commerce_order', $order);


Other than those I don't think there's any way to accomplish it using the API.