According to Farm Animal Shelters, bumblefoot is: "...a localized infection in the foot causing bulbous swelling of the footpad and surrounding tissue. It can affect one or both feet, and can affect one or many members of the flock. Bumblefoot is an infection that is caused by an injury to the ball of the foot. As the infection progresses, the lesion enlarges and the ball of the foot and tissue between the toes becomes enlarged and swollen. There is usually a round scab on the base of the foot that, when removed, will allow pus to be drained from the foot. If caught early, the foot can be treated with wraps and antibiotics may not be necessary."
The way I understand bumblefoot, it is caused by a staff infection, which can also be dangerous to humans. A chicken will not keep an injury to the foot clean so it is subject to infection.
Don't expect any grass to be in the run after the chickens are turned loose in there. They will eat it to the roots even if they cannot scratch the grass out. Don't waste your time and money planting grass. And don't expect them to find a lot of bugs and such in the run after they have been in there a few days and stripped it. They will find some bugs and they will keep scratching and looking, but it really won't be a lot. They do need to be able to scratch though. It is part of their nature.
The way I understand your post, the entire area is covered with the crushed stone. They will make a solid foundation that drains well. You could put sand on top and it will really drain well and be easy to clean if necessary, but they will scratch down to those rocks. That is actually a great way to make a run floor, a layer of gravel topped with sand. It drains really well.
I do not have experience with bumblefoot and don't know how big a risk those specific crushed stones are. I don't know how worn they are or if they are still sharp. I do respect Speckledhen's opinion. She has knowledge and experience. My inclination is to recommend covering the gravel with several inches of sand and clear out an area and replace the stone with real dirt to try to influence them to dust bathe in that specific area, but I don't know how big the risk of bumblefoot is. Even with an area to dust bathe in, they will scratch everywhere. You won't stop that.
