MG is everywhere. I don't know that getting rid of the flock would do the trick. It's in the ground, although it is highly susceptible to bacteriostats and is easily killed. There are more...and less...virulent strains.
I had a silkie rooster that I finally had to euthanize because I could NOT get him over it...even with huge doses of Denagard. None of the other birds got it from him and he was certainly in close proximity.
The treatment dose is 16 cc (about 1/2 oz) per gallon of water. The preventative dose is half that amount. I give it to our whole flock for the first week of every month. Warning...it makes the water bitter and some of them don't like it. I add a bit of karo syrup to it to sweeten it up some and that seems to cut the bitterness.
If this was my flock this is exactly what I would do:
1. start them all on treatment Denagard and keep them on it for 10 days. You will probably be amazed at how fast the symptoms go away.
2. Add the following to your layer crumbles:
One ten pound bag of calf manna (
Tractor Supply)
One 5 pound bag of BOSS (black oiled sunflower seeds) (wild bird section of
Tractor Supply)
One 10 pound bag of shelled seed/nut mixture (wild bird section of
Tractor Supply)
Mix these bags together and add 2 cups of this mixture to every gallon of layer crumbles. This will increase the protein, fat, oils and vitamins in their diet.
3. Keep their coop as clean as you can and after you have finished the 10 days of Denagard, completely clean the coop, spray it down with bleach solution and put in fresh shavings
Best of luck with them...you didn't do anything wrong...this crap just happens sometimes!!