I'm not really clear on the goal here. If you want to use a sophisticated proportional control setup, you need valves that can be set to a precise open level, and you need analog outputs. Both of these are likely to increase the cost and complexity of your setup substantially. Since it sounds like you will just face small changes in flow, and since the changes are likely to be continuous, and since the response time will likely be limited by the speed of the valves, and since you want to use digital outputs, you really should just use a open/off/close type valve and change it's state using digital outputs based on whether your flow is under/equal/over your target flow.
In this case, the only reason to use PID is if you are worried about the duty cycle on the valves and you want to use a timer setup, where you, for example, check the flow status every two minutes and then run the valve forward or backward for X% of the next two minutes based on how far away it is from the setpoint. However, I doubt that's a big concern for this type of motor, and anyway you could more easily achieve the same goal (and preserve your ability to respond to sudden large changes) by just increasing the allowable error on the setpoint or reducing the loop speed.
