Fuel Pumps are an example of FlightSimulation simplification. The procedure for ordering fuel in the SIM is just klicking something in the Tablett or FMS. No Danger here. Despite that you are right - Fuel Pumps are off, until refueling would be finished.
And btw I know what you mean (OCD) - but like with a lot of other stuff in real life - there is the theory (flight manuals) and the practice (what pilots are doing). And sometimes things might be better done different than in the theory. But if you try to be to perfect in the sim you go nuts, because in the sim it is just NOT possible to fly like the real thing - at least not at the current state of the msfs. Too much is not working or implemented.