I didn't know Ellis Lab had codeignitor.com pointing to codeigniter.com! From the article, I can only say the author didn't try CodeIgniter for a couple of hour

I didn't know Ellis Lab had codeignitor.com pointing to codeigniter.com! From the article, I can only say the author didn't try CodeIgniter for a couple of hours otherwise he would know you are free to do pretty much whatever you want with the framework. I do use CodeIgniter for all my projects and I do write my own queries most of the time (I'm a query performance geek). I think the only thing you are not free to run away from is controllers but that's the basic structure of a (MV)C framework.