A flooded piston would be more reliable than a flooded motor IMO. Lots of reliability critical things like vehicle brakes use pistons. All you would need is enclosed tubing sufficient to withstand the internal pressure. Submersion shouldn't be an issue because the system already needs to be sealed - the pressure would cause a leak if it wasn't already sealed, and in fact flooding would reduce the probability of a leak by reducing the pressure differential.

If you keep sufficient water (up to the weight of the fuel) at the location where it's needed, the entire system needn't need a pump at all when called into action, just a tap - gravity would be sufficient. This is presuming that the fuel is kept at basement level for safety purposes, of course, otherwise you could just keep the fuel where you're storing the water. You can get by with less water and active pumping, since hydraulics are easy to turn into gearing (force multiplication) effects.