The idea that ad networks don't care about click rates and clicks generated by bots seems very incorrect and false on even a surface glance. The revenue from ad networks is based on advertisers getting purchases and through that validate a marketing budget. It would be crazy if the networks did't already have several system to handle bad data and clicks generated by bots.
In addition, the argument is that the extension is only punishing the publishers. What it really do is to change the balance between unethical ad networks and ethical alternatives. By only punishing networks that automatically track users, the more ethical networks become better in comparison and will give better returns for each dollar spent on marketing. One could call this strong arming the publisher to chose more ethical, but an other way to see it is to eliminate the race to the bottom and discourage a lemon market. We currently have networks that have no problem with infecting peoples machines with malware, advertising products to children, or target the sick and vulnerable. If I ran AdNauseam and it causes a single website to consider an alternative ad network, I would consider that a major win for the Internet, even if that meant a few % less revenue.
Considering that some site has already gone over to more ethical alternatives in order to resolve the problem of ad blocking, it seems we are already making steps towards this future.