I thought by "Email confirmation tool" that it was a plugin but you meant the core feature.
The thing here is you need a way to let the user know they have successfully confirmed their email address. That is the reason why you're not redirected and displayed a "Thank you - your email address has been confirmed" message.
Now, what some sites do is to redirect you to another page after a few seconds has passed. You'll need to hack the core to do so but it is not a complex procedure.
1. In this line add this code:
$topath = qa_get('to');
$qa_content['head_lines'] = '<meta http-equiv="refresh" content="5;url=' . qa_path_to_root() . $topath . '" />';
2. Replace number 5 in step #1 with the amount of seconds you want the user to wait before being redirected
3. Replace this line with this code:
return qa_path_absolute('confirm', array('c' => $emailcode, 'u' => $handle, 'to' => qa_get('to')));
That's it. Now the user is redirected to where they came from after 5 seconds.