Have you tried talking to the town about it? Your building may or may not be zoned as a commercial space. But if they're using a work permit to run the place, then they're probably not following all the rules for whatever type of shop they're running down there anyway. Contact your town's housing and health departments to see what they have to say about it.

Unfortunately, this probably won't go over well with the landlord or their employees, but your options right now only seem to be to fight them on it or move. If you have the money, it may even be worth it to consult a lawyer to see if you could be entitled to compensation.