Since you can't disable the customer portal login interface, one method that works well is to upload HTML to be used as the "Login Message". This HTML is pretty limited in what can be contained within it and the allowable markup. If you write the markup in the document and it's not rendered to the browser, it's not allowed.
This basic solution provides an effective way to dissuade customers from using this login page any longer by making it more apparent that there is another mechanism which should be used and provide them great messaging about your new and improved Site interface.
The idea is that the HTML fragment has some great messaging and then a bunch of line breaks to push the login control well off the bottom of the visible area of the page so that the user doesn't see it immediately.
One manageable downside to this approach is that you will need to modify this document in each of your environments (sandbox, etc) so that the hyperlink to the Site is correct for that environment.
A sample Login Message Document:
<img src="/img/seasonLogos/2013_summer_aloha.png" />
<p style="font-size: 6em;">
Welcome to Acme Inc.
</p>
<p style="font-size: 4em;">
This Customer Portal login page should no longer be used!
Click the link below to visit our new and improved portal.
You won't be disappointed!
</p>
<a style="font-size: 4em;" href="https://www.google.com">
Link to Fancy New Site (Google)</a>
<!-- push the login control well off the bottom of the screen -->
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