MG is very common in backyard flocks. I would not cull all my birds for a positive MG test result. It can be controlled by closing your flock to new birds, or to birds leaving your flock. That is something to consider - never being able to add to the flock? Not a good position. Others I have spoken with about this also suggest starting over, including my Vet. I do not want to discount your input to this topic, but thus far you are the only person that has NOT said to "start over". I have read papers on CRD recently - they never get over it. "The hens will become symptomatic any time they are stressed, or even mildly sick from another cause." Also stated, "at some point the disease will surface and weaken the bird to the extent even antibiotics will no longer save it."
Wild migrating birds can spread the disease. Eggs for eating are fine to be sold, but not for hatching. I also wonder if starting the antibiotic before the culture was taken would skew the results. My Vet says the swab test will still be good. "Plenty of bacteria culture in that foamy eye."