The article has a pretty obvious slant in one direction. A lot of times small businesses will require this of their entry level workers not because they are afraid of their workers going to a competitor, but don't want their employees to go and start a competing business, which in the small business world is a very real risk. It costs much less to start a small business, and in the local market many of these small businesses operate in, a new competitor can take away a big chunk of an already small pie. If that competitor did so by stealing your business practices, then congrats, you are putting yourself out of business. I'm not necessarily saying this is wrong or right, but it's the other side of the story the NYT didn't discuss.
Ironically, I worked for JJ in college, and never once did this ever concern me. This may be my personal bias, but I think the NYT is trying to make mountains out of molehills here. There are much bigger contributing factors to low wages for fast food restaurant workers, such as illegal immigrants depressing wages, limited ability for workers to organize, and perverse tax incentives that prevent profits from working their way down the economic ladder.
As a side note, JJ pays better than a vast majority of fast food restaurant chains. Their in-shop workers are paid above minimum wage (average around $8.50), and it's fairly easy to move into a delivery driver position where you can earn $25/hr on Fridays and Saturday nights.