If the Supreme Court rules it as legal then the networks are up a creek without a paddle. Cable/Satellite/IPTV providers may decide to roll their own solution similar to what Aereo does for their markets and tell the networks to shove their retransmission fees.
Just like with autohop, what Aereo does is probably legal. But, unlike Aereo Dish (and DIRECTV/Cable) want other channels from the networks. I could see the networks withholding their cable channels unless Dish (and others) pay the retransmission fees. If Aereo does indeed win the the Supreme Court, I do not see Dish and others being able to get around the retransmission fees.
I would not be surprised if the new Dish/Disney contract included a clause preventing Dish from using an Aereo technique to avoid retransmission fees.... And I bet similar language is being put in every contract with every cable company.