Don't be discouraged by all the licensing rig-a-marole.
(I know this is a little off topic for the cheese forum--though more people being licensed means more good cheese to buy and eat!)
You will want to have dairy waste separate from your home septic system because the fats and proteins in the whey and waste milk will break your septic. You will need some other type of system---depending on the volume--perhaps dry wells, or holding tanks to pull solids and disperse liquids over a wider area (sort of like drip irrigation), or pigs to take your whey!
The key thing is to come up with some numbers in terms of your expected water use and waste and start talking with your inspectors about that, and it will probably take a while to sink in for them. They're accustomed to cow dairy which typically uses an extraordinary amount of water for cleaning equipment and moving waste, and generates considerably more milk waste during cheese production.
If you're hand-milking a dozen small ruminants and making <1000 pounds of cheese a year, your system profile is just a speck in comparison to most other farming operations.
Keep up the good fight.
Paul
THE BIG FARM Creamery
www.thebigfarmcreamery.com