I can control my fans so the food don't go down overflow. So in your case if you can't control either side to prevent food to go down. It's ok to shut it off. How big is your tank?
i read that you should shut your pumps off during feeding for 15 min to keep food in the water column. i shut mine off. you just use the stand by on vortechs or controller
I have my controller set to turn off return and skimmer and put my vortechs on feeding mode for 30 minutes. After 30 return comes back on and vortech's resume. 5 minutes after that skimmer comes back online and 30 minutes later, vortechs go to smart-ntm for 30.