After the 9/11 attacks, President Bush drew a curtain of oblivion against all the errors and mistakes that had led up to the attacks. There was accusation and counter-accusation in the media, but at the official level there was no recrimination against president Clinton's decision not to kill bin Laden when he had the chance, no action against those who had failed to stop the 9/11 hijackers from entering the country.
If Obama proceeds to take legal action against those who did what they thought was right to defend the country, all that will change. Prosecutions launched by Obama will not stop when Obama declares "game over." If overzealousness under Bush becomes a crime under Obama, underzealousness under Obama will become a crime under the next Republican president.
This isn't about "overzealousness": it's about enforcing the law. Clinton not killing bin Laden wasn't against the law. And there is a difference between good faith mistakes and a criminal conspiracy to violate and make a mockery of the rule of law. That's why a real investigation of all of it - including the alleged results - needs to take place and take its time. Give it two years to report, to allow emotions and tempers to cool. Then and only then make a decision on prosecution, so that there is no scintilla of haste or heat.
One more suggestion: ask Patrick Fitzgerald to run it.