It's been hard to find confirmation of the reports that the scanners were turned off. However, typical Thanksgiving eve wait times at airports are long, and the news was reporting very short waits at all airports. I expected the TSA to schedule an abundance of screeners on Wednesday to get ready for the opt-outs. It seems that they did do that and also limited the number of scanners in use.
Aside from the anecdotal tweets, this article states that there were a lot of screeners and not many scanners at Newark. However, this article from Wired cites many airports with the scanners in use, but commenters note that there were two obvious lines so that passengers could choose whether to go through the scanner or metal detector. I wouldn't be surprised if the TSA reacted in this way to the protest to be able to claim that there is widespread public support for their security methods, but it's impossible to tell if this is what actually happened.
By the way, I'd love if some disgruntled TSOs would start becoming whistle-blowers. I, for one, promise to protect anyone's identity who requests it. But, if you don't trust me, there's always Julian Assange.
UPDATE: NY Times has a good critique of the data.