I think in your case maybe you should wait until it seems she is 100% and then put the crate in the run for a while each day for a couple of days, so they can get used to her again. Sounds like you have a small coop. Mine is huge. It is an 8X16 cabin I renovated into a really pretty coop, with a 16X20 run. So, I have no problem putting a big dog crate inside my coop when I need to separate anyone from the flock (broody hens hatching eggs)
Then, maybe after a couple of days go down at night and slip her in on the roosting pole with the others. I didn't keep my hen separated but one day and she wasn't harassed by the others at all. But, you have kept yours out a while.
Hope she continues to improve!