Water – replace the thermopile with a thermocouple in the water heater, and have it work properly

I suspect you have a set-up like this?

You are concerned that when the water gets pumped back into the "water heater" it could possibly pollute your main water line?

The only thing I could suggest is putting a check valve on the "cold" water supply so that it can only supply fresh water. That is helpful if the pumps output pressure is higher than your supply pressure (This could happen on someday with low supply pressure or if you do not have main water pressure regulator)

In this situation the return is a dedicated port on the "water heater/boiler" and there should already be a check valve/pressure regulator/non return valve just before the water heater. So the rest of the house will run just on the cold water supply and never get any recirculation contamination.

Safest and easiest repair is to purchase a replacement at the hardware store. It isn't worth trying to repair a part that primarily functions as a safety device.

You may need to replace the valve if your existing thermocouple isn't removable or if the warranty is expired, bite the bullet and replace with a new unit.