I had c.diff with my colon and with my j-pouch. The treatment used for my c.diff was the same, the antibiotic Flagyl. I had to take 4-5 courses of it to get rid of my j-pouch infection. It was more difficult to treat with my pouch.
I don't know what pill you are referring to. I do know that fecal transplants are very effective and if I ever get another infection I will use that treatment. A hospital close by has simplified the transplant process. They use a donor's fecal matter, that has tested good for transplant, to make batches of frozen fecal transplant doses. This saves the cost of testing individual donors for each person with c.diff.