Are We To Believe The NIE On Iran's Nuclear Intentions?

I read the declassified summery of the 2007 National Intelligence Estimate Iran: Nuclear Intentions and Capabilities. I don't buy it.
The 2005 NIE said that Iran was intent on manufacturing an atomic bomb, the 2007 NIE says they "halted its nuclear weapons program" in 2003, ostensibly due to our military invasion of Iraq and subsequent deposition of Saddam Husein. Did our armies convince Iran to be good citizens or are they just hiding their activities better?
Much of this NIE reads like wishful thinking, as if those in the intelligence community would rather be writing policy than intelligence estimates. When I was a weather guy, a tool in forecasting was that you would predict persistence, i.e. that things will stay the same, unless you have twice the amount of reliable data to predict otherwise. This NIE is so drastically different in it's policy implications from the 2005 NIE, that I wonder what made them change their mind so abruptly.
Former ambassador John Bolton is not convinced either:

The real differences between the NIEs are not in the hard data but in the psychological assessment of the mullahs' motives and objectives. The current NIE freely admits to having only moderate confidence that the suspension continues and says that there are significant gaps in our intelligence and that our analysts dissent from their initial judgment on suspension. This alone should give us considerable pause.