The inherent illogic of stuff like this makes my blood boil sometimes... Why would/does Google penalize content from ranking just because links to affiliates or other sites do not use rel=nofollow? Either the content on the page is useful and it deserves to rank, or it doesn't. I don't see why having links lacking rel=nofollow alone should be a determining factor in that decision. Using rel=nofollow is a technicality.
If Google determines that the links on a page are against their paid-linking policy, then they should just discount any "link juice" that might get passed on from them. That's something they could do transparently in the background, without having to force Webmasters to consider this ridiculous rel=nofollow tag, and without having to deprive searches of valuable content (assuming Google otherwise determined it to be valuable except for the non-rel=nofollow affiliate links.)
Alas, the Google insidiousness continues, and we continue to begrudgingly comply forthwith so that we may get some rankings love! Although the whole thing does remind me of the pied piper sometimes :)