Before you shorten the one pin, reassemble the pins into the pump and hold the pump in place in the crankcase with no O-rings. if the pump seats tightly against the case, it should be OK. (I remember a little bit of play in these bores, with the bores being slightly longer than the pins so they can "float", but I could be wrong).
Also, is the pin damaged at all? Roll the pin across a sheet of glass and look for any wobbling. If the pin is damaged your best bet is to replace it. Just a thought, in case it may have gotten cocked during the last reassembly.