Google does see site.com, http://www.site.com as different pages. Even if you get links from all your partners to the www. site it’s possible someone can submit your site manually. I believe this trick is just as worse as getting bad links.
To get around the issue put a 301 redirect in your .htaccess file. I’m not an expert on 301 redirects myself so you’ll have to do a search for the info. basicaly redirect your www. site to your non www. site or vice versa.