"Ms. Miller learned about Valerie Plame from a confidential source or sources whose identity she continues to protect to this day.
That's my guess too.
Here's the options. Miller is protecting:
1) Wilson/Plame
2) An administration source
3) Another reporter.
If it's an administration source, you have the BIZARRE case that the NYT is protecting the administration, whose head they have called for on a pike.
If it's the other two options, the NYT and MSM have a LOT of explaining to do.
I think it's possible to disassociate the individual actions of Judith Miller from the management of the NYT. It is therefore not unreasonable that Miller is protecting a confidential source in the administration, possibly at CIA, who confirmed Plame was the originator of the Wilson trip.