You could hook some javascript to the page's onscroll event. The javascript would send ajax calls back to the server that record which comments have actually been seen (although there is no way to judge if the comment was actually read). It would be a bunch of work though, because the raw log would be enormous and so you'd have to create a special batch processing job to get the view counts split out for each separate comment.
That said, upvotes per page-load-including-the-comment is probably still better than the raw number of upvotes.