The Nature article does have reader comments below it, if you have some time. There's quite a few.
You can find a compilation of reactions to the Nature article at A Blog Around the Clock, which includes this pithy comment:
...PLoS has no intention to in any official way acknowledge the existence of this article (according to the old blogospheric rule "Do Not Feed The Trolls")(.)
There's also a lengthy post over at The Questionable Authority on the subject.
My only comment for now is to repeat the mantra that led me to start this website.
Ideas that spread, win.
Additional: Greg Laden has compiled things that Nature has published about PLoS over the years here.