Basically, to get rid of EMI you need a very pourous metal such as nickel (commonly used to shield against EMI). You can buy EMI shield spray. It works fairly well at eliminating EMI completely. I think yahoo shopping has it. Anyway, because water is polar by nature, any magnetic fields that are generated by the pump will give water a charge which is what you're experiencing. You would have to coat the inside of the pump with the spray stuff as well, but then you may not have an operable pump.
The only thing I can think of is add a large concentration of a nonpolar liquid to your coolant...
-Zoson
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