Being completely fair, if that happens, it usually is because they were in the book process, and it is very practical to save your Atma in the gearset so if you switch jobs you don't forget to reequip when you stumble on the right FATE, and they should have the right weapon with them as well, just going "Hey NIN I think you have the wrong weapon equipped" would solve all issues and not require you to leave, if they don't after that it's a whole other issue.
You could cite a Job Rock missing as something just as severe that can't be easily fixed while inside the dungeon.
