Why was Guinan on the Enterprise in "Yesterday's Enterprise?"

A deleted line from the original script explains that she's been with him (as a trusted advisor, tactician and confidante) since the year that the war began, e.g. 2344.

She moves closer to him... and if there is a sense of quiet power from Guinan that seems almost evangelical, it is intended.

GUINAN: Picard, we have been together for twenty-two years. I have been your advisor, your confidant, your friend and in all those twenty-two years, I have never led you astray. This time line cannot be allowed to continue. I've told you what you must do. You have only your faith in me to help you decide.

As to what she's doing on the Warship Enterprise (aside from acting as Picard's sounding board), the answer is that she's running the canteen.