Allowing your codebase to develop organically is a lot better than trying to fit the square peg of your domain into the round hole of the chosen framework.
Its a fair argument to make but honestly I've never worked on a web app where I didn't think that using an MVC framework like Django or Rails made sense.. Do you have any examples of web apps that would be better off without a framework than with? This follows from my experience with building F# libraries, but the ideas are quite general and can be useful in any programming language.
This is just not true. The whole article really doesn't apply to any mainstream programming languages like ruby, python, java, javascript etc. The author seems to be coming from an academic view point and the points he makes really don't translate to the software engineering world.