Voltage spike in pump/fan combination killing fan
You are right, a pump is a motor, a motor stores energy in its windings, and in its movement's energy. When disconnecting power, this energy has to go somewhere, hence the voltage spike (which can and does burn a 12 V fan, at nearly four times its rating). 

The spike is positive because your pump's driver circuit behaves like a diode rectifier when not powered.

A flywheel diode would not help, but a fast diode (schottky) in series with your pump could, and a capacitor in parallel with the pump would help reduce the voltage spike level.