Oz, I have a slightly different view of intestinal health than do most people.
I refuse to use drugs on them. I use a lot of yogurt instead. I use the unprocessed, unpasteurized 100% organic apple cider vinegar as someone suggested, in their water. Their feed is fermented with the same cultures.
There is an old adage that perhaps you have heard... "An ounce of prevention is worth a pound of cure."
With your situation as it is, with a full blown outbreak, you will probably have to treat with what is immediately available. If you have goats around there, put your kitchen gal to work making yogurt to put a little in all of your animals' feed and it will go a long ways toward keeping these outbreaks to a minimum.
At times of stress (such as moving them to new coops) a day or two before you know its going to be done, increase the amount of yogurt in their diet as stress causes the bad bacteria to explode in the intestinal tract but if they had a big gut load of beneficial bacteria, the bad ones wouldn't stand a chance.
I hope I have not offended you in any way with this, if so, please know it was not my intention at all. It is just something I feel quite strongly about. Also, it may be something the common person would have better access to if a problem should develop in the future.
I'm with you... I refuse to use antibiotics and such.. but, I eat my birds and eggs.
Oz is a breeder, and his stock is valuable in breeding... That sort of changes things, in my eyes. If I had valuable birds that I had no intention of eating, I would probably be less hesitant to throw medication at them.
My flock is currently dealing with respiratory illness... not sure what it is, or was, as they are starting to get over it.. guessing MG/CRD.. I just CAN'T justify tossing antibiotics at something that they will remain carriers of anyway. It just defeats MY purpose of having chickens: healthier eggs and meat without all the added stuff. I don't breed though. I don't sell birds. Flock is pretty well closed, save for the lone accidental rooster I rehomed last year. I purchase chicks in spring.. but they don't leave.
I totally get what you are coming from though, I feel like people stare at me like I have three eyes, when I refuse to just toss some Tylan at whatever cough they have.