This is a Washington Post article that is pretty interesting. It's long though.
Some things of note...
-We've trained and equiped over 80 countries since 9/11/01. I hope they don't use it on us
-The CIA has been involved in the killing of over 3,000 terrorist suspects in the same time.
-Of all the contries identified as a countries Terrorists would flee after Afghanistan was taken, Irag is conspicuously absent.
-In the future some CIA agents may spend their whole career living in another country with little or no contact with the USA to fit in and infiltrate. I would think it could be easy to forget who you're working for under those circumstances.
Here's the article if you want to read it...
http://www.msnbc.msn.com/id/10091295