Well, it the War itself doesn't have to strictly follow one of the routes. Sure, it'd be easier, but you could always come up with another scenario, where Shirou ends up unable to confide in anyone else.
Well, it doesn't have to be a confession. It could just be "chance" meetings they have, where Ayako notices small but concerning changes in Shirou's behavior, but won't let him alone about it, hence the meetings. Or something.