A one way fence or something similar, that the smaller, younger birds can escape too, but will prevent the bigger birds from following will really help. This allows the chicks to be out of reach, but still in sight, or out of sight. They need a break outside of the coop, or they will just stay in the coop.
However, even when the two groups tolerate each other, they will still remain a sub flock until the chick begin to lay eggs. That causes a status rise, and the flock becomes one. This is even true of chicks raised under a broody hen in the flock. The flock gets used to them and learns to tolerate them, as the broody hen will aggressively defend them. After she no longer cares for them, they are still accepted as one of the flock, but they are much lower in the pecking order, and act as a sub flock. Once they begin laying, they all become one flock.
Mrs K