You must bleed out the air trapped in the coolant system after a flush. Otherwise there will be air bubbles trapped in the coolant system and this can cause an array of problems. I'm not sure about a32 but for a31 you can find the bleed nut quite easily, it should'nt be that hard to find for the a32 somewhere on top of the intake manifold you should be able to see a nut with a sticker that says do not open when hot.
A tell tale sign when you have air trapped in the cooling system is when you start hearing boiling or bubling sounds from your engine....they usually call it gastric!
Am not sure why your mech is scared of damaging water pump, a flush isnt that drastic....maybe you could try another workshop that handles alot of Nissans or a32 specifically. I'm sure the rest of the forumers will be able to help recommending.
Cheers