You could replace the checkout with Payments Standard but you will need to take into account the user login part of the checkout. Currently users are required to login to checkout and are forced to do so. If you wanted to keep the order history and other data intact you will also need to force the login.
In addition to this you will also need to make use of an IPN page to insert the order summary and order details to indicate the order was successful. You will want to model the store order summary and details after the ones existing on the confirm page.
If you do it like this you should still be able to use the functionality of the back end for order and user reporting.
