Exactly right. This is not an argument to not use Django.
I think a lot of us have come to the same conclusion as this author: the abstractions frameworks provide are often too high level. Very quickly the needs of your project cannot be served by their generalizations. Especially in a language like Python, it's often easier just to roll your own systems.
However, starting off with a framework is a great way to get off the ground quickly. If you were to write everything from scratch from the beginning, you might burn out before you even produce anything usable.
Personally, I think CherryPy is the way to go. You're probably not going to need to rewrite HTTP [1], so that's an abstraction layer with which I'm comfortable. Everything else will need to be easily customizable for your project.
[1] Unless the threaded model doesn't work for you, like it doesn't for our chat backend.