Is this the only rooster you have? Was he at the top of the pecking order? You said the brooder you are keeping him in is in the coop - is it separated with wire so they can still see him while he is in there?
It sounds like he may have lost whatever place he may have had in the pecking order. While he is separated, make sure he can see them and they can see him.
I would remove the scratch from their diet. It really should only be an occasional snack, and not part of their regular diet.
Find things to keep everyone busy in the run - if there is nothing growing in the run, cover the ground with raked leaves or freshly mowed grass and then sprinkle some Black Oil Sunflower Seed through out it a couple of times a day. You can do a search on cannibalism and find many suggestions for things to add to the coop/run to keep them busy. Some feel more protein will help, and it certainly won't hurt. You can do that by feeding them all scrambled eggs, yogurt, fried hamburger meat, etc. to up the protein.
When he heals and you reintroduce him, I suggest trying pine tar - it's used to treat horses hooves and you can find it in most feed/livestock supply stores. Slather his legs good with it. It is nasty to work with, and the others will find it nasty to peck - you may need to reapply in 2 or 3 days until they get reconditioned NOT to peck his legs.
My problem was mostly solved by free ranging. If that's an option, you will likely have good success with it as well. If not, I suggest keeping them busy and entertained in the coop and try the pine tar.