I just thought of something: Maybe Quorra doesn't need to "use the facilities" after all...
I mean, Sam bled red human blood even when he was in the computer world (that's how Rinzler knew he was a User), so apparently one's basic bodily functions are the same, whichever world you find yourself in. Thus Quorra, in the real world, might look like she has a human body but in reality she keeps the advantages of her "computer self" - meaning she doesn't need to eat or sleep or relieve herself or anything like that.