People tend to have really strong opinions about feed (among many other things

I know I also feel strongly about the choices I have made and there are lots of food choices. Medicated vs non medicated. Layers vs. Non layer. Organic or not. and on and on and on. What I personally recommend is you read about what these chemicals actually do on a basic science level and then decide for yourself what is best for your flock and your situation.
My personal opinion based on a lot of reading is that the medication in medicated feed is only a mildly effective preventative and unnecessary for a small, well maintained backyard operation where living conditions are clean and healthy. I do not like to give medication where it is not needed. Good sanitation is the best preventative.
It is clear by searching the forums that people who use medicated feed still sometimes end up with cocci. Same with people who don't.
http://www.wisegeek.org/what-is-coccidiosis.htm
If I were you I would start by doing your own research about what cocci is (it is a parasite not a bacteria) and what preventatives and treatments are available.
The most common medication in medicated feed is Amprolium.
Amprolium is a preventative not a cure. It is a thiamine blocker. Thiamine is vitaminB1. This medication does not kill worms it prevents them from reproducing. Some medicated feeds also have antibiotics. I would be wary of those.
http://en.wikipedia.org/wiki/Amprolium
http://www.mypetchicken.com/backyar...edicated-feed-all-about-do-I-need-it-H74.aspx
There are natural options that are available that are also preventatives and not cures and are also only mildly effective. Pumpkin is one of them. Pumpkin seeds are coated in a chemical called cucurbitacin which kills some by not all types of internal worms. I do not know if they kill cocci or not. Pumpkin and squash are commonly used for overall good digestive health, which is never a bad thing.
I have never read anything that indicated fermenting feed caused bacteria problems as this is the growth and promotion of GOOD bacteria. The goal with pumpkin, ACV and fermented feed is not to directly fight cocci but to naturally create a very healthy digestive tract in which it is difficult for cocci and other parasites to thrive. This is a pretty good explanation of AVC.
http://rawgirltoxicworld.com/2010/0...-cider-vinegar-a-parasite-killas-best-friend/
There is not necessarily a wrong choice, just whatever choice is best for you and your situation.