I can understand your confusion over this sentence. I indulged in some head scratching, as well.
My impression is that the reference to the special prosecutor is third person -- it was only when the SP asked Judy the question that Keller himself learned his reporter was actually involved.
Seems to me the awkwardness of the expression evolves from Keller now embarking on a spin mission of his own -- asserting that he had "no idea" Miller knew "anything about anything". As if her being subpoenaed in the first place was all a big mistake. In other words, this whole farce has been "Judy's fault...not mine."
But, if that's the case, why was the Times so enthusiastic about one of their own going to prison "to protect a source." It is as if Keller is asking us to believe that he believed Miller wasn't involved and had no source...at all.
The year probably dates from Miller's discussion with Taubman, when she evidently contended that she had not been a conduit for a misinformation campaign.
Of course, since that time, Judy has evidently forgotten everything she ever knew about Flame...and might've told Keller at the time...if he'd only asked...
At any rate, Keller is trying to re-configure the story, so that it doesn't redound negatively on the Times (or him), shedding any all blame into Miller's lap.
My head hurts...
Mine does too. I've really given up trying to predict where all this is going and will just wait for events to unfold over the next week. But I will state that something much bigger is going down under the surface and we are just seeing a few superficial manefestations of that reality.