I just ignore the cleaning guy, go in a stall, lock the door and do what I need to do. I have privacy and if it bothers him he can leave. I've done it several times. Usually they just stand there with their mouths hanging, they can't believe it. I don't see the big deal, after all, that's what stalls are for - to protect your modesty.
Oh, and if questioned, I bring out the nuclear artillery: "bloody diarrhea." Those two words will back most anyone off. As in "Yes, I could have gone across the store to the other one, but it's likely I would have had bloody diarrhea all over the floor of your store." I've decided not to be embarrassed by the combination of a physical condition I cant control and other's stupidity.