Reno - 4:12 am on Mar 10, 2010 (gmt 0)
If Google allowed webmasters who have identified themselves as site owners to disassociate their websites from certain links then malicious link attacks would be drastically reduced.
You are exactly right, and they have the mechanism in place to make that happen.
Allow siteowners to log into G Webmaster Tools > list all backlinks > check a box next to each link that should be discounted > confirm
That would make it clear to G that the siteowner did not request and does not want those links, and thus, no need for any penalty whatsoever.