I don't know any natural remedies (though I've heard on here that giving a lot of powdered milk in the diet can help when there's an active infection). I'm going through a similar thing here trying to stay natural but up against it with cocci.
There are two levels to treatment, and the natural part is management. This will keep reinfection low. It means either completely changing their litter every 24 hours or moving them to new clean ground. However while this will help stop new infection (cocci in the droppings need 48 hours on the ground to become infective), it doesn't help an active infection.
You can leave the infection to run its course (about 5 days) but you may lose most of your birds, or they may never fully recover and always be small and unproductive. Some may be perfectly fine if it's only a light bout, but it's hard to know how bad things will get when they first get droopy.
This time around I chose to treat with a chemical coccidiocide... But in future I'm going to be more stringent with management (e.g. I'll try to stick with hens rather than artificial brooding, and I'll make sure I don't leave the tractor in one spot to start with). That's just my preference; but once chicks are infected and sick the game changes totally, in my view...
Hope this helps,
regards,
Erica