The argument really boils down to this: if the CIA has to worry about being investigated for its actions, the burden will weigh heavily and make the agency's work that much more difficult.
An AP article posted at MSNBC summarizes it:
In their letter, the former directors warned that the investigations could discourage CIA officers from doing the kind of aggressive intelligence work needed to counter terrorism and may inhibit foreign governments from working with the United State
What we have here is a serial killer requesting that detectives not search for hair and fibers, fingerprints, or other kind of DNA left behind at the crime scene. Can you imagine what would happen if they found something incriminating? It would put the serial killer in an awkward position and make stalking and killing his next victim that more difficult. Potential accomplices will shy away, and potential victims who would have otherwise died and been dumped in the woods will continue to live out their lives in relative peace.
No wonder the CIA is upset.