The woman with three eyes is not in the dungeon, but in a prison cell in the building in the bottom right of the fort. You need to interact with the iron gate door of her prison cell to talk with her.
It's currently not planned, but when I add new options to previous parts of existing events, I add a temporary reset option into the update to allow people to change their path if wanted.
Moriko was a bit of a unique case, as she had a choice already but the good path itself wasn't added until waaaay later.
Not everything will be available at the armory. You need to fight in order to get the higher quality loot. But as Genji pointed out, not all equipment is available at the moment. Otherwise I'd have no more rewards left for later battles.
An earlier version had such an option in the book next to your bed, during the skilltree update, but it was removed in a later update.