As mentioned in the article, that works if you can identify every spammy link. Without a penalty, you can make a million spammy links, let the filter catch 95% of them, and reap the benefits from the ones that get past.
That system isn't exploitable to sabotage another site's rank, but it also doesn't work at preventing link farms (as evidenced by most Google results before the recent change).
It doesnt take a genius to realize that when you identified 1 million bad links to XXX, and your database has 1.005 links to XXX, you should look carefully at the remaining 5K. Cross reference those sources against other suspicious links and so on.
Basically fight source of bad links, not recipients.
That system isn't exploitable to sabotage another site's rank, but it also doesn't work at preventing link farms (as evidenced by most Google results before the recent change).