First off, they did provide notice. I received an email about this at all the addresses I have an account under. Maybe the the author didn't and that sucks but this seems like an edge case and he is one of the exceptions, not the rule.
Second, you can turn this feature off which brings me to my next point. Even if they do decide to change this can you really blame them? The thing is we're all using the service for free and on top of it they're willing to share revenue with users. I mean we can't just expect every free service to never monetize. Could they have done it differently? Sure but lets not give in to the temptation to be armchair CEOs here and proclaim that we know that a different model would have worked better for everyone. I give Disqus the benefit of the doubt that they did their homework and decided that this is the best way for them to monetize and still do right by their users.
I use Disqus on my personal blog and I use it as part of an app I'm quite passionate about. In my app (link is in my profile) I use Disqus in much the same way Tumblr does where you enter your short name and your public pages can have comments. As someone using them in these two different ways I empathize with the author especially when it comes to my app as I don't want the ads associated with anything I'm personally doing but at the same time I'm not blaming Disqus either. I use them, in both cases, as an alternative to rolling my own. Their platform is far richer than anything I could do so even if they didn't allow opting out its still a win for me.
In the end this outrage is unnecessary. Disqus made no secret of this, reached out to us, provided a way to opt out, and even offered to share revenue! On top of that they're still a totally free service that's offering us value. The author himself says his blog will no longer have comments because of this. Why? I'm sure he can create a commenting system himself but obviously Disqus is delivering value in a way that's pretty tough to replace.
Come on guys, its one thing to not like these ads but to not use Disqus in protest really isn't hurting Disqus as much as it is the person who stops using them in most cases. They definitely acted in good faith on this one and we need to stop acting like every free service on the web owes us the service we want, how we want it, when we want it. This isn't a charity we're talking about here, its a web startup. I follow jaquesm's blog and I agree with most of his thoughts but I can't get behind this one.