Troubles with Reintegration after an Injury

Hello everyone!

To start off, I have been reading the forums, but newly joined today! My boyfriend and I have a flock of 6 that were born in late April. We have two Rhode Island Reds, two Plymouth Barred Rocks, and two Easter-Eggers. Back on July, we had an unfortunate accident with one of our EEs and her leg was injured. We brought her in, nursed her back to health - slings, splints, and all (yay!), and for the past 6 weeks or so, we have been attempting to reintegrate her back into the flock, with little success. As a side note, her injuries are fully healed, so it's not as if they know she was hurt.

The smallest, one of the RIR's is clearly top of the pecking order now. She is the first to pick at Rosemary. We have tried it all. Granted, we have them in a small Tractor Supply coop, and we have placed Rosemary in a dog crate with all of her own stuff right beside them. When we are home, we either let them range, or surround both coops with chicken wire and let them co-mingle in a slightly bigger space. I am hesitant to even do the ranging now, as a couple of days ago we had a near miss with a hawk.

I think we are making progress, but as a newbie, I would appreciate some input based on the behavior I am seeing. I think what's happening is that they are "OK" with her now, but she is at the bottom of the pecking order. They have been co-mingling all day today since I am off from work. It is mostly peaceful, and she is in with the others. Occasionally, one of them will come over and peck at her, which sometimes causes another (or all) to do the same. She looks like she is seeking a way out, or she flies up to a roosting bar. She has been able to successfully spend the night in there, and last night, one of the others spent the night up on the highest bar with her.

Is this pecking harmless? We have been so afraid to leave her in there when we aren't home (we are typically gone for 10-14 hours for work). I notice that they only peck at her once or twice, then move away from her. She isn't afraid to go into the coop, eat the community food and drink the water. I have given them fruit and vegetable distractions as well as CDs hung. We do plan on building them a bigger coop - this one was a birthday gift from my boyfriend's Dad, so we sort of became chicken parents before we were ready! Learning as we go here.

I would appreciate the input from you chicken experts! Thank you in advance!!

~Kristin