Some of the most critical insights we need to hear are in direct opposition of established institutions.
Sometimes these institutions are powerful in themselves. Other times, they may not hold far reaching power, but the ideas are most obvious from within the organization itself. So the people who have the knowledge to actually justify an idea are the ones with something to lose.
I agree with you completely. From a ‘benefit to society’ point of view, the cost is way too high for this to become the norm. But even from an individual site’s perspective, controversial (but insightful) comments are the kinds of posts which really validate the user community as one which is critical and open-minded. They often contain critical insights about the world we live in.
It is important to decrease trolling and poor comments, but are you losing more than you are gaining by forcing real names? Especially when there are alternatives. Some effective tools already exist, like good moderation and feedback/karma/ratings. Innovation in these areas, to improve them, is the way to go - rather than giving up and removing anonymity.