I don't think anyone has ever had a problem with explicitly asking and allowing users to opt-out. Apps that do that shouldn't be lumped in with the other ones.
Which ones are lumped in? Facebook and Instapaper are explicitly mentioned as examples of apps that prompt for permission before accessing the address book. Instagram, Foursquare and Path's prompts are only mentioned in passing, but those apps only added a prompt after the original story broke a week or so ago.