Thinking it over, the end result if this arms-race is a death of sandboxing as advertisers will require back-end access to the service you're hosting so it's completely indistinguishable from your content. Any other proper isolation of ad content will be detected as ads.
The real sins, the true annoyances and the routes for malware, come from ads brought in from off-site. Ad copy served directly from the domain to which you've gone are rarely a problem. But when that domain sublets part of their page to an agency, which in turn sells exposures to anybody including malware vendors, then you need to block. Your innocent visit to wanteddomain.com ends up with literally hundreds of scripts and images pulled in from tens of unrelated domains. So an ad-blocker needs only to block cross-domain calls to be effective _without affecting display of ads from the source domain at all_.