Traffick reports on the over-hype of Google Autolink and I agree. Autolink is just a tool. You have to turn it on to make it work. If you don’t like it, turn it off. That’s from the user perspective.
From a web site owner’s perspective, I can understand some concern, but no where near what some bloggers are ranting about. If you really don’t like it as a site owner, add the Autolink blocking JavaScript. I think that’s reasonable.
If you don’t want Google to index all or part of your site you have to add a noindex meta tag and/or modify your robots.txt tag don’t you?