There is a very simple reason that we shouldn't trust the national security establishment to act in good faith and be truthful. This is that repeatedly, when the truth eventually does come out, it becomes clear that they haven't been in the past.
For example, high level administration officials repeatedly lied about why Rahinah Ibrahim was on the "no fly" list. The truth: a simple clerical error. But, it took "seven years of litigation, two trips to a federal appeals court and $3.8 million worth of lawyer time," and false statements by high level officials including Eric Holder, for this fact to be revealed. A redacted version of the final court opinion can be found here.
Administration officials also lied about the extent of NSA surveillance programs and about their effectiveness.
Administration officials have been very misleading in their statements about how sexual assault cases are handled in the military.
Administration officials in the Bush administration lied about the claim that the Guantanamo Bay involved only high value prisoners, and about U.S. use of torture.
The Bush Administration lied about the connections between Iraq and 9-11.
The use of the cloak of secrecy afforded to National Security matters for improper purposes has historically been invoked for a very, very long time to hide mistakes, ineptitude, and human rights abuses in cases that almost never require such sweeping secrecy to protect legitimate national security interests.
While President Obama has had significant achievements in reforming domestic policy in a liberal direction, he has inexplicably mostly left extremely radical national security policies from the Bush Administration undisturbed.