Guess what: adblocking because some ads are obtrusive is like killing a fly with a cannon. Or more like killing a fly with a nuclear bomb. No adblocker maker is going to start whitelisting every single non-obstrusive ad network. They're going to block most of them. Most users will not make the effort of whitelisting their favorite websites either, they'll just see some adblocking app on the Top list in the App Store, download it and forget about it.
Bigger websites will get smarter about ads. Probably more "sponsored" stories and similar things that you can't block. Smaller websites are going to have a harder time tho. All because some people can't understand that if you don't like obtrusive ads the best thing to do is to stop visiting sites with obtrusive ads.