You can use htaccess to deny access to your site based on referer or IP. This way, if you have spammy backlinks to your website you can block the visitors coming from the website that links back to you. The question is if Google is also checking the referrer for that backlink or the crawler only builds a list of backlinks to your site and checks them separately. Because if it works by checking the referer you might be able to get rid of the bad backlinks. How do you think Google is handling this ?
Google builds a list of URLs to crawl. Then they crawl them. Google does not provide a referrer as they crawl. So, no you can't block links from counting or not counting - except by making the requested URL return 404 or 410 for all requests for that URL.
By testing the referer value, you can block some of the other visitors that come from those sites after they click the link on that other site. That's as far as it goes for now.