She figures out what happens almost at once, I can't imagine how traumatizing that must have been for her. The man she loved, the man she worked with sent her on a fools errand. He turned her noble quest into something dark and dirty. He made her a murderer and she doesn't know how to live with that. It is something that Faith will go through in the 3rd season of the show.
This is the first story in the Buffyverse, timeline wise, that isn't written by Joss Whedon. It was instead written by Amber Benson. If that name sounds like one you have heard before it might be because she played Tara on the show.