Rice states that the NSA retaliated for him bringing his suspicions to their attention, but it appears that he didn't follow protocol himself. It is wholly reasonable to revoke his clearance after he showed that he was even slightly unstable- the procedure is to suspend access until psychiatrists can verify that there is no threat to national security by allowing a cleared person to continue working. We have to remember that classification (and almost everything at NSA is TS) is determined by the amount of harm its release can do to the nation. He must have displayed the signs of someone who can't simply say "roger that" and follow orders. I'll bet there are some former colleagues and superiors remembering instances, that now demonstrate how disloyal he was.
If anyone is interested, you can google AR 380-67, which is the regulation on personnel security- covering all aspects of getting a clearance, keeping it, and losing it.
Essayons