I have a site that logs AJAX requests to Google Analytics (since that's essentially the only "page views" on the particular site). I was doing a test for if (_gaq) before trying to push into the array, because I wasn't more concerned with giving the users a good experience than tracking page views, and that did work if Google Analytics was being blocked from loading at all. Unfortunately, I eventually learned that Disconnect was causing that test to throw a JavaScript exception instead of just blocking GA from loading and leaving _gaq undefined. As you can imagine, narrowing down that it was Disconnect causing the problem from a few random users' "the site isn't working" complaints was a lot of fun...
It's not a huge site, but I do spend a couple thousand dollars a year keeping it online. I'll be damned if I'm going to spend that to keep a free site online and then feel bad about running some advertising and analytics to make sure it doesn't end up in the red.
Some find it to be more transparent, and in many ways it is, but really you won't see much of a difference between the function of the two. I personally use Disconnect, and have yet to find it break any sites. I find setting Flash to ask before being enabled on web pages tends to break more sites than anything else.