The article then launches into recommendations about requirements gathering and writing down your thoughts (functional specs anyone?) which kind-of sounds a little bit like the waterfall method to me. I believe the waterfall method has a bad reputation for overengineered and overcomplicated solutions. We have come full circle, again!
No matter the methodology there seems to be this behavior in the industry that as soon as some code does the job, regardless of how terrible it is, it must not be touched again and we must move on. Whether it was over-engineered because of bloated requirements gathering or because it was hacked into some sprint period the end result is the same.
My recommendation is this: Don't discourage people from refactoring code that already works. Good code will survive refactoring or even rewrites.