the intank fuel pumps are cooled by the fuel itself, so there should be enough liquid(petrol) in the tank to cool them off. when the car is on cng the pump keeps on running (to keep the fuel rail pressurized), and if the fuel is low the pump over heats.
now on the sun visor of your santro there should be a sticker mentioning to keep you tank half full all the time, you should follow that, the relay that you mechanic mentioned, should cut of the pump when the car is on cng, after that the pump should not fry, logically.
i think the relay didn't cut of the pump properly.
still you have no other option to get yourself a new or kabuli pump and keep your tank half full all the time.