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Using antibiotics when there is not a bacterial infection produces drug-resistant bacterial strains that are almost impossible to treat. It is better to only use it in situations where you know for certain there is a bacterial infection or a bacterial infection is very likely to occur.
I treated my chick because the place I bought some young hens, and some chicks from, had a bird that tested positive suspect of MG. My veterinarian told me to treat all of my birds, including the chicks and said if my chicks did not come in contact with it, it is safe to treat them and won't do any harm.
And if the chicks are dying, I'm sure treating them might not be much harm if it might save their little lives.
Antibiotics are the appropriate treatment for MG. MG is very infectious, so what your vet told you was appropriate for your situation. That doesn't mean it is appropriate for every situation. With no sign of respiratory infection (runny nose, bubbly eyes, odd breathing sounds) MG or other respiratory infection is unlikely. If what is killing the chicks is not bacterial, antibiotics will not save them, but will put them at risk for more deadly infections in the future.