In my opinion, there are some risks in going either way. I personally think there are more reasons to let mama raise chicks with a flock than to isolate them, but there is one condition. Mama has to have enough room to work. Chicks raised with a flock normally develop better immune systems and don't have serious integration issues later on. There are always exceptions, such as what pbjmaker mentioned, but if mama has enough room to keep her chicks from underfoot of the other chickens, she will keep the others from hurting her babies. What normally happens is that one of the other chickens will peck at one of the babies, mama will severely reprimand the offending chicken, the lesson will be learned, and all chickens then leave the babies alone. The only reason I personally would not let mama raise them with the flock is if I thought mama does not have enough room to work with.