Taken from another Alias forum, the following is from an insider who was close to the crew:
The script that Lena had signed off on was not what we actually saw on screen. Scenes were taken out due to the fact that TPTB were originally planning on having the finale be at least 30 minutes longer. Due to time constraints put on them by ABC, that did not happen. The storyline needed to be changed to accomodate this. Unfortunately the character of Irina was the one who suffered.