Your instinct is wrong

Just leave the 4 pin which used to controll the stock fan unplugged.
The pump is connected to the power supply and will pump a constant amount of water through the loop. Aquastream pumps can be set to a fixed frequency via usb or Aquaero, by default it is set to automatically find the optimal frequency. I don't know what kind of pump you are using but it should suffice to connect the power supply to the pump.
Water temperature (ultimately your card temperature) is controlled via the fans which are mounted on top of your radiator.
Slow fans = higher water temp = higher component temp
fast fans = lower water temp = lower component temp
You can use any fan controller or an Aquaero to controll fans.
An Aquaero got some other neat features.