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?

Also there are plenty of PHP codebases that were developed "organically" (i.e. without a framework) that are absolute eye sores to look at because without a structure in place its too easy for developers to write bad code.