What is the risk of leaving a well pump on a 3-wire system?
edit:  @Ed Beal pointed out that this may be a 220V pump motor.  The answer below is based on the assumption it's 120V.  Now that I think of it, Ed's probably right, the question is talking about 3-wire vs 4-wire.  

Connecting neutral to the ground at the device is a terrible idea, dangerous, especially around water.  It really ought to be fixed.  I'd turn off power to the pumps if you are doing anything around them.  

The simple way to make this safe (and NEC compliant) is to install GFCI protection on the circuit using the existing wiring.  

However, there is a catch:  if the GFCI protection trips, the well pump and the septic pump will not be operational until someone manually resets the GFCI.  The pump motors may be susceptible to nuisance trips.  

Another catch: if the wiring is replaced, depending on local code, you may be required to install GFCI even with a ground wire.  So you may be getting GFCI either way.