Do you not have a seperate run that the injured chickens can go into to keep them safe, We had a problem last year, so i spoke to someone who reares them as a living, this is What he advised split the garden into two sections with chicken wire so they could all see each other but could not harm each other, at night they slep in different coops but can still see each other, switch the bedding every night so they all got used to each other smells, and then after a couple of weeks, when it was dark i was to go down douse every chicken with vinegar and warm water and put them all back together,
The breeder did say to me as long as they have enough room to escape form the one that is pecking them, I was to leave them well alone chickens pecking order does change, and they do challenge other chickens and they hate to be spied on.
good luck.
p.s
(My 2 cockrels sleep together all the time)