There's no reason why Irina wouldn't kill someone who was protecting the Passenger--if he was protecting the Passenger from her.
We really can't tell exactly what transpired now--obviously the "official" version is a cover-up of some sort. However, Irina certainly could have killed him--and there's more reason to believe that she would have killed him than Jack would have (his colleague, and someone known to be a little more judicious with lethal shots, although he's certainly capable of delivering them!). Say Vaughn Sr rescues Nadia from the KGB and Irina has escaped. There is no reason why she wouldn't kill Vaughn to get Nadia back for herself--knowing that Jack would want to take Nadia away from her. (What, do you think that they would automatically be working together as one, big, happy family?) Even if it were the case that Jack assisted in Irina's escape (which, being open-minded, I consider to be a possibility), there was obviously a betrayal involved in the escape somewhere (for whatever reason) when she went to the KGB.
However, to me, the larger problem is the problem of Jack's knowledge of Irina's survival. There's no way that he'd simply allow her to rattle around the world unmonitored. His agitation upon realizing that she was alive was real--and if it wasn't about the tires, then it must have been a realization inspired by Sydney's revelation. If he didn't believe that she died in the accident, he must have somehow been convinced that she died at some later time.