Wow. This is a model article. It takes two controversial opposing articles about an extremely relevant problem, points to a grey area that's worked in the past, and then, quite insightfully, points out a missing link (self-hosted advertising that is still inherently auditable to third parties) that we should fill in.
Even though I detest advertising, I think a lot of what I detest about them could be seriously mitigated by turning advertising into something a business plans and designs for. Let's get some applicants to Y Combinator next season that try to figure this out.
Unfortunately, it's not really a missing link. :) First, it's not that easy to run the entire ad server stack for every advertiser. Many want their own DoubleClick tags in regardless of what setup you have, since they're running campaigns on multiple sites and want to track them in the same place. We call these third party ad tags and they cause no end of technical problems, but it's not going to change anytime soon.
Secondly, running your own ad server really just guarantees that your specific ads will end up blocked by the vast majority of people running ad blockers. There is an entire Easylist ruleset specifically for site hosted ads: https://hg.adblockplus.org/easylist/file/8811cd8afb56/easyli...
The only unblockable way of showing ads to people is by selling sponsored content. It's shady as hell, but many sites do it.
This is why we ran our little experiment to hide content for people using AdBlock Plus on Friday night. We wanted to see how many people noticed (a lot) and we wanted to know how quickly Easylist was updated (about 8 hours).
Even though I detest advertising, I think a lot of what I detest about them could be seriously mitigated by turning advertising into something a business plans and designs for. Let's get some applicants to Y Combinator next season that try to figure this out.