Without seeing a picture of your setup I'm just going to throw a couple things out here.
I'd leave the gravel - mainly for drainage. We have clay here so if we don't get the water out it turns in to a swamp.
They're going to eat it from time to time, don't think it's really something to worry about. Ours eat all kinds of rocks/grit/etc. Mine also seem to love eating the clear silicone caulk around the house when they freerange, which drives me crazy.
If possible, I'd cover a good portion of the run (if not all of it) if you can. If you can keep them dry it'll cut down on the smell and make for cleaner/healthier chickens.
I'd leave the gravel - mainly for drainage. We have clay here so if we don't get the water out it turns in to a swamp.
They're going to eat it from time to time, don't think it's really something to worry about. Ours eat all kinds of rocks/grit/etc. Mine also seem to love eating the clear silicone caulk around the house when they freerange, which drives me crazy.
If possible, I'd cover a good portion of the run (if not all of it) if you can. If you can keep them dry it'll cut down on the smell and make for cleaner/healthier chickens.