First of all, Johnson's attorneys responded to that argument, by noting that the handbook clearly stated it was not considered to be a legally-binding contract. I suppose it will be up to the court, to rule on whether it was, or not, (if they haven't already).
More importantly, (perhaps MUCH more importantly), NDA's do not typically protect against "whistle-blowing." They normally protect against the disclosure of trade secrets. Though Alcor's attorneys have argued that Johnson has violated some sort of trade secret issues, I don't see anything in that book that even remotely resembles a trade secret, (though I do see a lot of what I would call "dirty laundry").