That is a difficult egg to crack. It may mean the end of turn-key ready-to-roll websites - but if the 'digital media industry' is genuinely worried about extinction, they should already be looking at ways to make their ads safe and palatable, rather than continuing the ads-arms-race.
I take a lot of comfort knowing that I'm not uniquely intelligent - and honestly, some of the work-arounds advertisers have come up with for getting around ad blockers are pretty clever. Restructuring how a business works isn't the same thing as inserting an ad, but there are plenty of very intelligent people already involved in the industry. I would like to see the 'worried about extinction' folks make some proposals about alternate ways of doing business. Up until this article, most of the ad-blocker news coverage has gone just short of callling ad-blocker users baby-killers.
From time to time, I'll fire up a vanilla web browsers in a VM to see what an unprotected browsing experience is like, hoping to see things calming down (I want companies to be able to monetize their websites! I didn't even opt-out of Slashdot's ads until they started yelling at me), but each foray sans adblocker is more miserable than the last. I would think that an organization would strive to avoid associating their product with misery, but this is exactly the opposite of what the ad industry has done to the web.
Finding a way to get ads in the hands of small website owners is a difficult task. Even more difficult will be convincing content consumers that the ads are safe and unobtrusive again.