The most likely and simplest explanation for why the CIA destroyed the tapes of its torture sessions with Abu Zubaydah and Abd al-Rahim al-Nashiri — even in the face of strong reasons not to — is that the tapes showed evidence of serious crimes. If you were a CIA person caught literally red-handed, would you rather be at risk of obstruction of justice charges, or of charges of torture, war crimes, or attempted murder or who knows what. That simple decision tree leads straight to burning the evidence.
But in the name of baseless speculation, I offer you the following more baroque hypothesis. The not infallible David Johnston tells us that,
… in April or May of 2002, officials briefed on the classified details of the case said, C.I.A. officials expressed dissatisfaction with the pace of the interviews and concluded that Mr. Zubaydah was revealing only a little of what he knew. C.I.A. interrogators, led by an outside consultant, ratcheted up the use of aggressive techniques.
Outside consultant? Where does the CIA go to get expert help torturing people? I doubt somehow that they went to Haliburton or even to Blackwater USA. They may have had an aging contra or El Salvadorian death squaddist on the payroll, but the real up-to-date expertise is probably in the Middle East.
So maybe part of what the CIA was hiding was that they got a Syrian, or a Saudi, or even an Israeli, to help them?