Well there are a couple of things you can do. Space and hideouts, multiple feed and water stations, some out of sight. If she is hiding in the nest, I am thinking that you might not have hideouts in the run.
With a pecking order, birds need to get out of sight of a higher bird. The higher bird, pecks the lower bird, or makes like she is going to peck, and the lower bird gives way. She leaves the feed bowl, acknowledging the pecking order. Think of it as curtseying to the Queen. Now I have seen them make a circle out of sight, come right back and eat right next to the Queen.
The problem in a lot of runs, is that they are just a 2 dimensional open rectangle. There is no place to get out of sight of the other birds, so there is no way to acknowledge their lower position. What can happen is the higher bird takes this as challenge, and continues to attack the lower birds. It can get ugly. You want lots of hideouts, but not traps, each hideout needs two exits. A pallet up of cement blocks, can give smaller birds a place to eat, without bigger birds. The larger birds can get under there, but it is tight, and uncomfortable, and generally they will soon leave. A pallet leaned up against the wall, can allow a bird to rest without being chased, behind. Roosts in the corner of the run, can allow birds to use the 3rd dimension of the run, height. Currently I have a pallet set up on saw horses, so that birds can get under and on top. I lean a pallet up against this, and gives some shade in the late afternoon in summer. A piece of plywood, set up like a small wall, with a food station behind it, so that birds at the main feed station cannot see this bowl.
These are things in the run, that allow birds to survive integration and make more use of your available space. Birds do get tired of each other if kept in too tight of confinement.
Also, I am pretty sure that the longer you keep the injured bird separated from the flock, the worse her integration is going to be. Adding a single bird is very tough. Get some blue Kote and get her back in there ASAP. Or more than likely, you are going to have a very drawn out affair.
Mrs K