You can destroy a dungeon with Naturalize 2. Doing so removes that dungeon from the game and removes its owner’s venture marker from the game. Nothing prevents its owner from venturing into that dungeon again if another spell or ability instructs them to, though they would have to start from the topmost room again. Note that each dungeon has a single owner; even if two players are venturing through two dungeons with the same name, each of them owns a separate dungeon card.