Conceptual question about taxonomy structure
If I understand the question correctly you want to prepend the city name as an argument on the view, so you would have:


  organisations/denver/yogashops


well you could equally have the city appended:


  organisations/yogashops/denver


The question has no mention of Views, but I would recommend that you create a view with the contextual filters of organisation and city:


I recently set up something similar for global dealerships /find-a-dealer/europe/fr