I'm NPIP, and as a breeder I've already agreed that, in the case of Mareks*, I will destroy my flock, decontaminate, wait, and then consider starting over. I understand that's pretty extreme in the view of some, but better that then to spread the disease further.
Where did Mareks enter your flock? If you purchased from a local breeder, they may need looking into. Coccidia are everywhere, and opportunistic - likely became uncontrollable when your chickens were already suffering from Mareks, and their immune system became weakened.
There are some people who maintain closed, Marek's positive, flocks very successfully. All their birds need to be vaccinated, and the vaccine doesn't prevent Mareks, it merely prevents the worst outcomes of Mareks - you frequently end up with a flock of carriers. That's not something I am personally willing to do.
Good luck, whatever you decide - and seriously consider looking into the source of your birds as a potential Mareks vector.
* and a small number of other diseases. A I of course, also Mycoplasma gallisepticum and Mycoplasma synoviae, and Pullorum-Typhoid (which hasn't been seen in commercial flocks in decades).
