Hey Alan  by how much does

 Hey Alan 
by how much does the value change? 
you could add another transistor between the PWM output and the TIP 121 which would reduce the load the TIP121 is putting on the arduino, which may then reduce the effect it is having on the Irms value. Or yes Im sure you could do something in software especially if the change is always the same: if (pumpIsOn==1)  Irms = Irms - change;
I like the sound of using the flow of water to represent energy use, that would be really cool!

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