A staff memo from NPR's CEO Vivian Schiller said that "Ellen Weiss has notified me that she will be leaving her position," but gave no reasons. The outside review—after all that time—concluded that Williams' firing was legal. It recommends a review of NPR's ethics code and some other typical mushy corporate measures, but it does not say anything about Ellen Weiss' handling of Williams' dismissal.
The fact that she fired him over the phone was a mistake. But it seems like a mistake rather minor to end a career over. If NPR itself really felt that she handled it that poorly, it should have asked her to resign when the incident happened, not months later. And if it wanted to wait for the results of the independent review, then one would have assumed that that review would give some reason as to why she should resign.
Update: A tipster tells us that just a few weeks ago, Weiss was interviewing candidates for an assistant job to her and a couple of other people in the news department.