I think the main problem is this pervasive habit (not talking only about disqus here) of making controversial modifications (because hey, they must know that a significant part of their users won't like it) and making them the default. I don't think that the OP would have minded so much if the feature was turned off by default. It's like social networks changing their privacy options, and making everything public by default.. but with the option to revert to normal when/if you realize what changed.

As for the second point, the fact that the ad links are similar to all others: that really IS sneaky, however you look at it.