Are you saying that the bilge pump is running constantly?
Or, it actually sounds like you want to disable the auto function? If that's the case, why?
But... just remove the fuse (or flip the breaker) for the auto side of the pump.
If you remove the ground... won't you also be eliminating the manual control of the pump? In "most" cases, there is a single ground with two hot leads.
Oh... you said you disconnected the grounds from the "battery"... don't you have more than one battery?
Does one of the battery's have a ground that goes to a bus bar? I can't say what is going on with your boat, but best practice is that accessories are NOT all grounded via a battery terminal... instead through a common bus bar. Look for that.