The OP article mentioned 2000 people signed a anti Starbucks petition. I'm quite sure the new bakery will serve more people than that on a daily basis.
Then you have the comparison to the ice cream parlor and Casey's Corner. Both of which have corporate sponsors. Edy's is not hated here, Why? It's owned my the largest food company in the world. It's also a "modern" company with respect to the Main Street "theme".
Worse things have happened. Like putting Johnny Depp inside a classic Disney ride. Some say that bold change made the ride better. People want Star Wars and Marvel in the Disney Parks. But remodeling a bakery on Main Street U.S.A., and "plussing it" (Walt's words) with a sponsorship and product from one of America's premiere companies is supposed to be bad? I don't get it.
Perhaps those up in arms now understand how many of us felt over the Depp thing. I personally got over, and even excepted it, even though I've never seen a single POTC movie. And as for the bakery thing. I have no problem paying all that money for a Disney escape, and still being able to enjoy my favorite Starbucks beverage. For most of us, it's the best of both worlds.