Ok, so I'm going to try hack it myself.
The plan is to call the confirm.php page with cURL so that moodle confirms the user behind the scenes.
What I don't know is where to put the code to call the confirm page. I'm thinking it should go in signup.php just before
$authplugin->user_signup($user, true); // prints notice and link to login/index.php
How does that sound? Crazy?