Can water ruin a fuel pump? Maybe. I'm skeptical. As you are probably aware, air slips into the tank as you burn off fuel and that air can contain a fair amount of water vapor -- especially in humid climates. The water then condenses on the cold walls of the tank at night and ends up at the bottom of the fuel tank where it is sucked up by the fuel pump, mixed with the gasoline and burned harmlessly. (Some of it dissolves in the gasoline and is burned that way)
Folks in cold climates frequently dump a pint of isopropyl alcohol into their gas tanks in the late fall to help dissolve and get rid of the Summer's accumulation of water in the tank before it freezes and causes trouble. Fuel pumps have to be designed to deal with the worst cases of water accumulation in the fuel tank. And Toyota tends to build their vehicles like tanks. Their fuel pump probably will not be flimsy.
So, maybe the fuel pump is damaged. And maybe it isn't. You should at least hold open the possibility that the folks at the dealership don't know what they are talking about.
You can either have the fuel pump replaced which may not be outrageously expensive. On many Japanese cars, the fuel pump is quite accessible and can be replaced without dropping the fuel tank. Or you can get a second opinion from a good independent mechanic. Or you can do your own checks if you have some basic tools, some time, and the inclination.