I have this same pump at work so I know what you are talking about. Easy way is to use a relay, specifically a DPST relay, apply 12v to the common pin, connect the NC pin to the pump, the no can be left floating, connect the coil to the arduino (ideally via something to isolate the inputs on the arduino from the back emf). When arduino is connected and the coil is activated no 12v, pump runs. disconnect arduino the relay goes off and supplies 12v to the pump, pump turns off. Additionally, if you dint activate the coil, the pump remains off.
Sorry for any typos or what not, sent using my phone.
ACtually, with the minipuls3, you just have to short the two pins on the motor start/stop to start the motor and open them to stop it. This is even easier because you can just use a simple NPN to short them. Remember to control the motor from the back, the pump has to be stopped via the front panel.