most/all pop-ups are bought on a cost per impression basis (CPM). not a cost per click basis. so, your plan wouldn’t piss off advertisers. if anything, you’d give them more clicks and their alexa/nielsen netratings would go up, which would help them sell more cpm based advertising.
attacks on sites that serve pop-ups might work. have some kind of reporting tool in the browser that reports back what sites have pop-ups. then, send enough traffic to bring down the server. And/or have some kind of system that warns users going to the site, that there are pop-ups. Alexa actually keeps stats on whether publishers serve pop-ups. Publishers will learn to not serve them.
Of course, browsers would probably not be able to differentiate between spyware generated pop-ups vs site generated ones. So, this system might unduly penalize publishers.