If they have all been living together then there is little point really in separation if the problem is infectious. Any similar symptoms in the past within your flock?
Some respiratory infections are very infectious but this doesn't necessarily mean all the birds will succumb. Did your vet give a diagnosis or was Baytril prescribed as a broad spectrum antibiotic to catch all infections? (primary and secondary infections, antibiotic therapy is often prescribed as supportive treatment in some cases where the primary cause is mycoplasma for example)
Separation does also depend on your poorly bird however, if her symptoms are quite severe then separation to prevent bullying is a good thing if you feel that putting her with her flockmates would be detrimental to her health.