That will work fine. That's how it is plumbed on trucks with a diesel. All modern cars and trucks have multiple coolers (trans, p/s, engine oil, etc) that runs the engine coolant thru them to bring all the fluids to the same temp (the eng temp). Also to bring all the fluids up to temp faster. If you use the heater exit line that is not the "hot" side it is the cool side. The water pump does not pull fluid it pushes coolant thru the motor. It will not disrupt the cooling system, you'll just add some capacity.