Separating birds is always a pain, but it is a fairly successful practice. But the choice is either that, or culling the aggressive bird, or culling the submissive bird. It won't kill Gertie to be there. Do not think that you are punishing Gertie, she is not smart enough for that concept. What you are doing is making her a stranger to the other birds, so that they will attack her when she comes back in. The theory, is that she will be so busy defending herself, that she won't have time to pick on the submissive bird. Sometimes it works, sometimes it doesn't.
You do need to watch the flock carefully now, because sometimes a strange thing will happen, another bird will begin to pick on the submissive bird. If that happens, it is often an indicator that something is wrong physically with the submissive bird. If this happens you need to cull this bird, and get on with things.
Flocks are tricky to blend together, and some don't ever fit. When combining your flock, you really need more space than the suggested 4 feet in the coop, especially this time of year, when they are roosted up in the coop due to the long dark nights. Measure your space and count the total head. Even if you free range, in the winter, that is a small amount of the day. Mine are roosting up at just a little past 3:30 these past few days.
Sometimes the change is enough to make a bird become aggressive. Sometimes a couple of days will work, but often times when you put them back together, you are back to the original problem in days. The thing is, while this is just between two birds, it causes tension in the whole flock. You may have to do some culling to get a peaceful flock.
You may have to cull one bird or the other. It is the tough part of chicken keeping, wishing they just would all get along, does not always work! Ugh!
Mrs K