Steve...old post, but the php code appears the same here in the latest version of moodle. I commented out lines: 61-63 as you illustrate:
if (!empty($signup)) {
$this->content->footer .= '<div><a href="'.$signup.'">'.get_string('startsignup').'</a></div>' }
But the "create new account" link still remains in the login block. Checked it twice on the server. Any ideas?
Also, I have set my authentication to "manual accounts ONLY"....perhaps a future version of moodle could tell the login block that "create a new account" may NOT be link I want to display if I have gone to manual accounts 
Ken