thrylos, I guess I don't understand why you think the Twins "don't owe Rochester" anything, beyond what they're contractually obligated to provide... but you think the people running the Rochester organization DO owe the Twins something beyond what's in their contract. Rochester is, I believe, a community owned organization, and their ability to maintain a quality facility relies on income. The crapfest that the Twins have provided recently, in terms of talent, has meant Rochester has lost revenue, so if they have a way to generate more revenue by selling merchandise of a team that's popular with their community fan base, I don't see why they "owe" the Twins anything that would be beyond what's in their contract either.
If the Twins had a problem with an affiliate selling another team's merchandise, they need to include restrictive language in their contracts with affiliates. Of course, most minor league organizations would likely tell the Twins to shove that language up their ass and sign a different team.