I wouldn't not run the bypass. With out it the would be no circulation with-in the engine until the thermostat opens. This will cause hot spots and pump cavitation.
http://auto.howstuffworks.com/cooling-system2.htm
http://www.woodyg.com/fairlane/finfo...ngsystem4.html
"Water Pump By-pass Hoses"
The water pump by pass hose connects the water pump to a fitting on or near the thermostat housing. Coolant may flow in either direction through the by pass hose, depending on rpm and degree of open of the thermostat. When an engine starts cold, before the thermostat begins to open, coolant moves through the engine with out an exit route. We know that we want the coolant to stay in the engine block until fully warmed, but some coolant must circulate. If stagnant, unable to circulate, localized areas in the cylinder heads can boil coolant then super heat it and cause metal failure. The by-pass hose offers a partial escape route for coolant to circulate back through the engine while the closed thermostat will not allow it into the radiator."