Exiting the dungeon was already a feat worth of praise even for a heavenly rank hunter like Medusa, but doing so while protecting both Emma and the guide they recruited made things even more difficult. To make matters worse, Medusa was also carrying a passed out Tina Celes on her back. If it was for Medusa, she would have left Tina on the army's care, but Emma insisted on bringing her along because she suspected Tina had information that could become useful for their mission.
It took them a while, but Medusa knew her way across the third world better than anyone since it was the world she first landed when she came with Jon. This allowed her to reach the 'emergency exit' in record time in spite of her circumstances.
The cathedral outside the dungeon was still destroyed and it would remain like that for a couple days when Uriel would eventually come out from the dungeon and fix it by crushing flux orbs in front of it.