If you're a founder and looking to sell your company, is there anything you can do to guard yourself against these kinds of situations? I imagine it might be some particular part of a golden handcuff / golden parachute deal, but making it work for everyone involved sounds super hard...
Sure. Don't sell your company. Don't take it public, either. Principled moral stands are not compatible with making as much money as possible.
Net neutrality is supposed to help small- to medium-sized internet companies do better. Taking a stand on net neutrality is therefore not incompabitible with maximizing profit in the long term. It is, however, usually incompatible with maxmimizing quarterly returns for myopic investors.