First, control which scripts are loaded
The most important reason to block ads is to protect yourself from malicious, dangerous and incompetent code delivered through these ads. Accordingly, script blocking is a far better method than ad blocking (alone). Once you do that, you can leverage that tool for fine-grained control.
Let's first assume that you block all scripts completely. That massively reduces the amount of checking the site can do, because all checks must now be on the server-side. But ads and content are normally served from different servers for a variety of reasons, so you can expect very little interference. Theoretically, a site could hide all content behind an initial script that must be executed first - but that would reduce the performance drastically and nobody wants that.
Of course the modern internet is unusable without some scripts. But the result of the previous discussion is that it's also pretty unusable and insecure with too many scripts. The solution, then, is the good old middle way.
So here's a good plan of action: First, load the site with all scripts disabled or only scripts from the same origin enabled. Mark ad network domains as untrusted sources to help filter the lists. Then enable sources temporarily one by one if functionality is missing.
Note however that there is a learning curve. Which sources are necessary for fancy fonts or other very important content (tm)? Which one of the twenty-odd sources of the average site are actually ad-agencies, market research-sites, tracking-sites, or generally malicious? You may need some understanding of marketing techniques to classify them. Also, many scripts are chain-loaded, so once you load a new script new sources will appear that you might need to sort further.
Then, control cookies
Cookies can be a nasty invasion of privacy but at least they can't break your system. And if you don't load scripts from a certain source, you don't have to worry about their cookies as much. But while most sites react nicely to missing scripts, missing cookies can create nasty, unpredictable problems. Faking them might be a middle ground, but I haven't tested that. I expect that to be a very brittle solution. Good web developers (no, that's not actually a natural contradiction) will encrypt their cookies anyway, so the easiest way is to sandbox them on a per-site basis and delete them regularly.
Lastly, be nice
It doesn't look like the need for ads will be going away soon. But right now there is an imbalance, and less technically versed people are "paying" for others by looking at more ads. In the long run, something will have to be done about that. Just ignoring the problem and blocking every ad will only get us on the "bad" side of the discussion once it comes. It also forces the market to use more and more malicious solutions.
A smarter solution is to use our knowledge to not only block malicious networks, but also to vet "good" ones. If you find one, consider putting it on a whitelist. Maybe while still deleting cookies, maybe only scripts that pass an automatic test, maybe only scripts with a certain hash... there are lots of ways. Of course using adblock-buster scripts is a bad sign, so Forbes should probably stay on the blacklist for now. But maybe others should not.