I did what James is recommending on two of my pools. Only time will tell, but they have been working well for about a year now..
You basically just use a water temp probe, like the one that comes with an EasyTouch.. Drill a hole in the pipe, stick in the probe, and use a hose clam to hold it in place. Wire it to the green and white wires coming from the cell (not from the flow switch).. Now the cell sees the water temp from the new probe and not the thermistor in the flow switch..
I used Scotchlok UR2 connectors so you don't have to strip the wires.. Just crush the button and the wires are connected.