The threat that President Bush issued in 2002 was due to Iran being a state sponsor of terrorist groups, which was true then and is still true today. Historians can argue over whether that threat was a good idea at the time but it's too late to retract it now. We have to deal with the actual situation as it obtains today.

As for what Iran's leadership decided and when, we really have very little visibility into that so don't believe anything you hear. We're not even certain which faction is really in control of nuclear weapons policy. (This isn't an endorsement of the recent attacks.)