This issue has been coming for years. I blame Google for starting it by getting people to worship at the little green bar. If they had never done that there would have been no metric that we could look at and say "see, I know what I'm doing". Each iteration after that simply made people more and more aggressive with link building. 10 reciprocal links are good, 100 must be better. 100 directory links are good, 1000 must be better.
Then you add in the fact that Google allowed sites that the search team hates to profit by using adsense and things get even more muddied.
I remember when the guidelines were slightly rephrased to allow for the possibility that a site could be harmed by links. Then we were able to do it. On a small scale in very specific scenarios, we could do it. Now it seems that we can do it in a whole lot of other ways. Questions have been asked directly to Googlers through private channels about ways to fix this and it is being looked in to, but the solution doesn't scale. At least not for webmasters.
This is why we changed our marketing approach a few years ago. We still build links like many others do, but we have a whole rack of other things that we do that work better, and faster, at driving customers to client sites so even if search engines vanish tomorrow, our clients will weather the storm just fine.