StratFor analyzes the cyclical nature of counter-terrorist operations in both the FBI and CIA:
(It) was a lack of intelligence that helped fuel the fear that led the Bush administration to authorize enhanced interrogation techniques. Ironically, the current investigation into those techniques and other practices (such as renditions) may very well lead to significant gaps in terrorism-related intelligence from both internal and liaison sources — again, not primarily because of the prohibition of torture, but because of larger implications.
When these implications are combined with the long-standing institutional aversion of U.S. government agencies toward counterterrorism, and with the difficulty of finding and retaining good people willing to serve in counterterrorism roles, the U.S. counterterrorism community may soon be facing challenges even more daunting than those posed by its already difficult mission.
Dirty work no matter how you cut it, and probably harder than ever in the current environment.