But there's another bazooka in the room: the contemporary erosion of trust in authority, in this case scientific authority. Ionannidis' remarks are for the best, I think, but will add to the confusion of not only what knowledge can the public trust but who is more apt to produce that knowledge.
Before things get better, this will inevitably widen the door not only for old bad science in new clothes, or in the form of professional, corporation funded research that resorts to p-hacking and such methods, but also to the further discredit of science in general in the general population.
Having said this, I do not believe Ioannidis' work (or Ben Goldacre's for that matter) is a tool of such agents.
Edit: After reading some comments in this thread, I have to say in all honesty that I suspect that the ACSH's interest in Ioannidis work is disingenuous, without putting into question the validity of his work.