It wasn't loosing her personally that did the damage
Our intelligence gathering has been hampered for a long time by lack of physical assets. Losing 1 isn't going to make that much of a difference.
It wasn't loosing her personally, but the connections that blowing her cover revealed. Anybody she had worked closely with would now fall under suspicion, so if she had recruited any informants they where now in danger.
Worse, the name of the company she worked for was blown as a CIA front company, and apparently this company was used by more then one agent over seas. This would create a domino effect of blown covers.
Our thinking that we can do it all with satellites and network wiretaps has and will continue to get us into trouble.
This NIE is a piece of work...it says they quit their weapons program...BUT they could make a weapon within 2 years. So what this tells me is they have a weapons program thats pretty well advanced to the stage of "we can make a weapon any time we want"...and the CIA is >guessing< that right now isn't the time they want to make it.
The NIE is always a piece of work. They are influenced by political fractions within the government that want to push one view or another.
And if Iran's stated goals for nuclear production are honest, they will have enough capacity to produce the nuclear material for a bomb at some point. They could probably do it right now if they pushed all of their production capacity towards making one low powered bomb. And for a national government that is really the hard part, nuclear material is very hard to make and decays over time. The rest of the bomb making is not easy but compared to making the nuclear material in the first place it isn't hard.