Thanks, +Jennifer Lin
I'm glad there's an official statement out on this, but it remains frustrating that all this discussion we're having about the reasons for the retraction isn't happening in the comments section for the paper and is thus inaccessible to everyone who might come across the paper in the future.
The major difference between my point of view and that of PLOS (and other publishers, too, I reckon) is where the decision to retract is extended to honest mistakes as well as deliberate deception. As a scientist and as a student of altmetrics, I know that the majority of the literature consists of honest, well-meaning but mistaken conclusions. The literature is not a solid foundation upon which to build, and by it's very nature cannot be. There is no scientist I know which assumes that any result in the published literature is necessarily replicable, so in the absence of partial retraction, I probably would have gone with an erratum, despite it being one of the major claims of the paper, or used some other mechanism which doesn't penalize self-reporting of mistakes so strongly.
So the main issue is how the extension of retraction to cover honest mistakes disincentivizes self-reporting of mistakes, and it's unfair given that so much of the literature is mistakes that just haven't been uncovered yet. The high-profile nature of the case is just why it got uncovered in this case.
I really did think PLOS had begun to move beyond thinking of themselves as the gatekeepers of truth.