“But in the case of the anthrax mutation in the beginning of the article, the mutation results in decreased fitness, thus represents a downgrade.”
Whether or not a mutation is a downgrade depends on the environment the cell is in. In an environment containing quinolones, the mutation is an upgrade since unmutated cells cannot survive. In an environment without quinolines, the cell is at a disadvantage since it cannot reproduce as quickly.
Your assertion sounds very basic and I have no disagreement with it.