I don't recommend doing this since there are a huge amount of things dependent on the fact that index.php works as the root of Q2A.
Still, you can try changing this line in qa-page.php:
'qa_root' => $qa_root_url_relative,
... to ...
'qa_root' => $qa_root_url_relative.'qa.php',
That will change the endpoint of the AJAX requests, including voting.