Yes, it takes 2 gallons of seawater to make one gallon of fresh water and that means a gallon of relatively concentrated brine. The solution is to pipe the brine out to sea where it will remix with seawater. There's no long term problem with this and in fact we already do this with treated sewage. I know it's not ideal but it's a pretty good solution, better than, say, cooling a nuclear power plant with seawater.