Disable registration on commerce checkout
Per Bojan's comments, leave "Allow guest checkout" checked and disable the "Guest registration after checkout" pane. We may need to update the documentation a little, but doing these things and then configuring your general Drupal settings to deny user account registration will leave you with a site that no one can ever register against and anonymous users can still checkout on.

(The fact that you don't see the checkbox to "Allow registration" in the "Login or continue as guest" checkout pane configuration is irrelevant, because it's disabled by default. You don't need access to it in order to disable the ability for guests to register prior to checkout.)

If you don't need this intermediate step at all, you can simply disable the checkout pane and the page will be skipped for all customers.