Seems like starting to franchise would not necessarily fit with their long term growth goals.
I'd assume this is mostly just about brand control. A store selling their products that they don't control will not necessarily have the experience they want for their brand. Even if they can't shut it down, just harassing them can prevent the store from growing very large and causing issues with their brand perception.
That said more media coverage around this could paint Trader Joe's as a bully and be more damaging to their brand than an unauthorized seller.