If you had been able to leave them with their mom, all this would be elevated, albeit the integration of the chicks as in my experience, she abandons them after about 2 months (Silkies) and goes back to being broody again. Those chicks are now on their own without mom to protect them in the coop, so we made a temp coop for them for a couple of months. They free-ranged alone in their group, and the adult free-ranged in theirs. It wasn't until they were 6 months old that they were the same size and weren't picked on anymore.
Once, we were in a different situation with winter coming, so put a wood box like a rabbit hutch in the coop for them. They'd hide in the box by night, then were the first ones out the door in the morning. They were starving and thirsty as they couldn't get to the food/water due to bullies, so every morning, I brought out their starter feeder and a waterer, and they ate/drank and headed out to free-range.
As for the mom getting back into the flock, I think they would eventually work it out themselves. They may have a changed pecking order now, but that's for them to decide. If that one hen that's the new boss is being overly mean, I'd put her elsewhere for a week or so, out of sight of the rest, then when she comes back to join the flock, the tables are turned.