It is more correct to say, "The food at Green Restaurant is cheaper than it is at Brown Restaurant"

I agree with Nina’s suggestion, but want to add that in my opinion “The food at Green Restaurant is cheaper than Brown Restaurant.” is not only less correct, but wrong, because you are then comparing the price of food with the price of a restaurant (what it would cost to buy the restaurant itself). It you want to make it short, “Green Restaurant is cheaper than Brown Restaurant” would be OK in informal speech, because people would understand that you weren’t comparing the prices of the restaurants, but the prices of the food they sell.