Actually, Joan Allen was never in Bourne Identity. I think you are referring to Supremacy. Her character, Pamela Landy, is the Deputy Director of CIA and becomes involved in the plot after one of her operations gets sabotaged by an assassin who uses Bourne's fingerprints as a decoy. It is then that she finds out about Bourne and the covert ops Treadstone and Blackbriar.
Getting back to the topic, yeah I see some resemblance.