Maybe it is the framing of the step as a "reversion" or "roll-back" rather than "spike" or "prototype" that is causing that sense. Personally, I would never throw away the code I spent time and effort writing just to stick to a systematized refactoring method like this "Mikado." I don't think the advice is unsound, and I have done exactly this many times in my own career, but instead of throwing it away I would shelve it, put it in a branch, write a document about what has been/needs to be done, and write a corresponding tech debt or feature/fix ticket for it with the new and realistic estimate.