This is a huge advantage. I want to be a disqus user, not a user of 4000 tiny blogs. When I make comments on x, y and z random blogs, I want to be able to follow replies to them in one central place.
I especially don't want to give a username and password to all these little poorly-secured blogs.
If you want to "control" "your" users, build your own comments system. And turn off RSS.