People with clearances also have huge incentives to lie to themselves about the decency of what they're doing. One of the main thing secrecy protects, is such people's morale.

You know what they say, "if they cheat with you, they cheat on you too". A liar is a liar. If your job involves seeking people's trust in order to betray it, you're not very smart if you think your boss wouldn't betray you.