Earlier quoted context omitted.
Whatever the case, you can turn it off: http://help.disqus.com/customer/portal/articles/666278#disco...
It should have defaulted to 'off'. You can break trust exactly once.
I don't know about you, but I can live with a couple of non-obtrusive links that go other places—especially since, like a lot of people, I got emails about it ahead of time. If you can't, you can turn it off.
You act as if the ads are putting ugly pictures of fat people are flooding your site or ads for e-Cigarettes or other skeevy things. I've been seeing them for months — their ads, far as I can tell, are of higher quality than the ones you see on Facebook and Google search. (I see links for Exxon, Comedy Central and Citi on a recent comment thread on my site. Certainly not bottom-shelf names.)
The reason why you probably didn't notice them is because they're so unobtrusive that they were designed so you wouldn't notice them. Now whatever philosophical issues that raises, I think, from what I've seen in my own experience, Disqus handled this the right way.
EDIT: I don't get the downvotes. My point is totally valid here.