WASHINGTON, Sept. 1 — An enduring mystery of the C.I.A. leak case has been solved in recent days, but with a new twist: Patrick J. Fitzgerald, the prosecutor, knew the identity of the leaker from his very first day in the special counsel’s chair, but kept the inquiry open for nearly two more years before indicting I. Lewis Libby Jr., Vice President Dick Cheney’s former chief of staff, on obstruction charges. Now, the question of whether Mr. Fitzgerald properly exercised his prosecutorial discretion in continuing to pursue possible wrongdoing in the case has become the subject of rich debate on...