It will be difficult to sort by votes globally, since this requires modifications to the database schema. However it is relatively easy to sort by votes within the page - add the following lines before the qa_content_prepare() statement in qa-page-home.php:
if ($qa_template=='questions') {
foreach ($questions as $key => $question)
$questions[$key]['netvotes']=$question['upvotes']-$question['downvotes'];
qa_sort_by($questions, 'netvotes');
$questions=array_reverse($questions, true);
}
An integrated (database-wide) implementation of this is on the roadmap.