1. Having bred and shown large and bantam cochins for many years I can say that I would never recommend plucking the feathers, I always clip the feathers and they have no issues breeding. If left to their own devices they wear their feathers down to short stubs during the breeding process, so I am just speeding up the process by clipping and getting chicks faster. If you pluck they may bleed, if they bleed and the other birds see the blood they will pick at the blood and eventually cannibalize the bird.
2. Pen them, chickens that will eat each other lack emotion on our level. Too often we attribute human emotions to animals, we are not animals and they are not humans. It is not cruel to pen them and in most cases prolongs their lives and protects them from predation. My birds are all penned, lay well and live up to 10 years or more.
I have several breeds and several varieties within each breed and all are kept separate for breeding purposes, each egg is marked according to breed and family line to ensure they are tracked, each chick is marked at hatch to ensure the family lines and breeding programs are adhered to for each breed and variety.