One easy way to provide a paid vs. ads system would be to streamline under a single business model.
One example would be a user generated content site that allowed users to "be their own advertiser", and pay in proportion to their traffic/clickthrough/CTA value.
Unfortunately, while this may be easier for you as a company/accountant/developer, users have indicated pretty clearly that metered billing is too damn confusing, for the most part. One possible way to alleviate this is to offer the site as free with ads, but advertise at an inverse rate to the user's "ad value" – thus, no one ever has to "pay in", but you still provide a cleaner/less disturbed experience for your highest-value users.
Come to think of it, plugging in a site visitor's Klout score/other reputation metric, and then turning off ads for people above a certain level of influence might even be a generally good idea, as it removes all distractions from your site/content/design from the people most likely to spread the word virally to the mainstream follow-on visitors you will actually monetize.