If, on day one, Fitzgerald merely asked the question, "Was Valerie Plame a member of the class which is sought to be protected by the statute?" And if the answer is "no" the investigation should have been shut down. Any supposed perjury would not have been about an integral part of the underlying charge since the underlying charge was inapplicable.
Fitzgerald, by calling Plame a "classified" agent in the indictment has apparently made his decision on her status.
As for the underlying charge, that might be important in an aiding and abetting charge, but it's not necessary in a perjury or obstruction case.
If you accept the underlying charge argument, you're giving defendants a green light to perjure themselves and obstruct investigations. Why cooperate if you can lie, derail the whole case and walk?