I run a church food pantry in NJ. Our usual practice was to help people shop our shelves but because we do not want people congregating in our pantry

A bit additional work, but you could print out a list of available food items and have people check off what they need and a pantry volunteer could collect the requested items. It would limit the number of people accessing the pantry.

Your usual practice is still good bc it maximizes use of good and minimizes discards bc people don't like an assigned item.
If you have waiting space, can you keep some people in there while you let others choose?