Isabella is orphaned and her betrothed just died a bloody death. She has been living at Otranto. Suddenly her would-be-father-in-law is chasing after her like an ancient evil human version of Pepe Le Pu. She makes it to the secret passage and plans to run for the Church. But what then? Would the nuns take her in? Would she cry "Sanctuary!" from the bell tower and live there? Would she ask a priest to sneak her out of there and take her to some distant town?
Not that I would expect a frightened young woman to be rational in such circumstances, but I'm trying to understand where she thinks she will end up if she can escape Manfred. What are some possibilities for her options?