I get how some people might feel like it's annoying to auto follow, but the reality is that most people don't care / notice that they're now following all of their friends. And at the end of the day, having friends using the same app as you does provide a better user experience which is why this trend has emerged.
You have a valid point about having friends in the app. However I'd imagine that there's a more elegant way of accomplishing this. I realize I'm a rare use case but I have thousands of Facebook friends many of which I don't want to know everything they're up to. I'd imagine many other people don't want to know everything all of their Facebook friends are doing. Perhaps someone should complete a more detailed study on this :)