I've said this before (on HN) and I'll say it again: a search engine that refuses to index sites containing advertisements absolutely kills off SEO.
What's the point of getting to the top of the search results if you are unable to monetise it?
The only way forward is to refuse to index sites with advertisements. Google will obviously not do this (and, in fact, to me it looks like they do the reverse - downrank non-monetised content - because it's in their best interest to serve sites with ads).