I am inclined to agree, plus something about her look did not fit in with the feel of the Bourne movies (but I think this was cleared up in Supremacy where she was given a more down to earth look).
Probably just a case of they needed someone up and coming, but would come cheap for a pretty minor role. Identity was filmed in 2001 and Stiles was just coming off the back of "10 things I hate about you" which was a somewhat successful chick-flick/teenager movie where her performance was praised.
Plus, apart from Potenta as Marie, there really is not any other female characters in this movie, so probably was added in for that also.