Really the best thing Nintendo can do to combat a stubborn developer like Beamdog is to make the Wii U such a smashing success that they look like childish dicks and ignorant fools for ignoring a popular platform that has already fixed 2 of the problems they had with the Wii.
It's not like NO developers have had success with WiiWare, at least in its infancy. The eShop is already getting a lot of love and high praise from indie devs, especially Nicalis and Renegade Kid.
Also, if they keep up the "I feel I have been wronged, therefore I will burn a bridge" attitude, they are going to find the industry to be a lonely place soon, as its not like even Apple is 100% perfect about their online store either.