I do not see any way that keeping her separate would make a difference to respiratory illness, if she was living with the flock before the incident. She has already been exposed to all the same things they have.
So I would put her back with the flock as soon as she is acting like her normal self. If you see bullying, especially if she gets sick and then you see bullying, that would be a good reason to separate her. Even then, it is probably best if the "separation" can be where she and the others can still see and hear each other: using a wire dog crate, or dividing the main pen with wire mesh, or something like that. (That is not always possible, but when it is possible, it makes re-introduction much easier than if she had been inside your house or otherwise completely away from the rest of the flock.)